From e2b2ac732f3692164d08ac32f88442d3e7a829ed Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 11:26:45 +0100
Subject: [PATCH 01/28] docs: add v1.0.0 release implementation plan

13-task plan covering robustness fixes, DDA support, new DIA-NN params,
InfinDIA groundwork, comprehensive documentation, and issue cleanup.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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+# quantmsdiann v1.0.0 Release — Implementation Plan
+
+> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
+
+**Goal:** Prepare quantmsdiann for a robust v1.0.0 release with DDA support, new DIA-NN parameters, and comprehensive documentation.
+
+**Architecture:** No new workflows or modules. All changes are additions to existing files — new params, flags, guards, test configs, and docs. DDA uses the same pipeline as DIA with `--dda` appended to all DIA-NN invocations. Default container stays 1.8.1; 2.3.2 is opt-in via profile.
+
+**Tech Stack:** Nextflow DSL2, nf-core, DIA-NN, Groovy, Bash
+
+---
+
+## Task 1: Fix tee pipes masking failures
+
+**Files:**
+- Modify: `modules/local/diann/generate_cfg/main.nf:26`
+- Modify: `modules/local/diann/diann_msstats/main.nf:21-26`
+- Modify: `modules/local/samplesheet_check/main.nf:38-43`
+- Modify: `modules/local/sdrf_parsing/main.nf:24-30`
+
+- [ ] **Step 1: Add pipefail to generate_cfg**
+
+In `modules/local/diann/generate_cfg/main.nf`, find the `"""` opening the script block (line 20) and add `set -o pipefail` as the first line:
+
+```groovy
+    """
+    set -o pipefail
+    parse_sdrf generate-diann-cfg \\
+    ...
+    ```
+
+- [ ] **Step 2: Add pipefail to diann_msstats**
+
+In `modules/local/diann/diann_msstats/main.nf`, find the `"""` opening the script block (line 20) and add `set -o pipefail`:
+
+```groovy
+    """
+    set -o pipefail
+    quantmsutilsc diann2msstats \\
+    ...
+    ```
+
+- [ ] **Step 3: Add pipefail to samplesheet_check**
+
+In `modules/local/samplesheet_check/main.nf`, find the `"""` opening the script block and add `set -o pipefail`:
+
+```groovy
+    """
+    set -o pipefail
+    ...
+    ```
+
+- [ ] **Step 4: Add pipefail to sdrf_parsing**
+
+In `modules/local/sdrf_parsing/main.nf`, find the `"""` opening the script block (line 22) and add `set -o pipefail`:
+
+```groovy
+    """
+    set -o pipefail
+    parse_sdrf convert-diann \\
+    ...
+    ```
+
+- [ ] **Step 5: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+git add modules/local/diann/generate_cfg/main.nf modules/local/diann/diann_msstats/main.nf modules/local/samplesheet_check/main.nf modules/local/sdrf_parsing/main.nf
+git commit -m "fix: add pipefail to all modules with tee pipes
+
+Without pipefail, if the command before tee fails, tee returns 0 and
+the Nextflow task appears to succeed. This masked failures in
+generate_cfg, diann_msstats, samplesheet_check, and sdrf_parsing."
+```
+
+---
+
+## Task 2: Add error retry to long-running DIA-NN tasks
+
+**Files:**
+- Modify: `modules/local/diann/preliminary_analysis/main.nf:3-4`
+- Modify: `modules/local/diann/individual_analysis/main.nf:3-4`
+- Modify: `modules/local/diann/final_quantification/main.nf:3-4`
+- Modify: `modules/local/diann/insilico_library_generation/main.nf:3-4`
+- Modify: `modules/local/diann/assemble_empirical_library/main.nf:3-4`
+
+- [ ] **Step 1: Add error_retry label to all 5 DIA-NN modules**
+
+In each file, add `label 'error_retry'` after the existing labels. For example, `preliminary_analysis/main.nf` currently has:
+
+```groovy
+    label 'process_high'
+    label 'diann'
+```
+
+Change to:
+
+```groovy
+    label 'process_high'
+    label 'diann'
+    label 'error_retry'
+```
+
+Do the same for:
+- `individual_analysis/main.nf` (after `label 'diann'`)
+- `final_quantification/main.nf` (after `label 'diann'`)
+- `insilico_library_generation/main.nf` (after `label 'diann'`)
+- `assemble_empirical_library/main.nf` (after `label 'diann'`)
+
+- [ ] **Step 2: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+git add modules/local/diann/preliminary_analysis/main.nf modules/local/diann/individual_analysis/main.nf modules/local/diann/final_quantification/main.nf modules/local/diann/insilico_library_generation/main.nf modules/local/diann/assemble_empirical_library/main.nf
+git commit -m "fix: add error_retry label to all DIA-NN analysis modules
+
+These are the longest-running tasks and most susceptible to transient
+failures (OOM, I/O timeouts). The error_retry label enables automatic
+retry on signal exits (130-145, 104, 175)."
+```
+
+---
+
+## Task 3: Add empty input guards
+
+**Files:**
+- Modify: `workflows/dia.nf:38,46`
+
+- [ ] **Step 1: Guard ch_searchdb with ifEmpty**
+
+In `workflows/dia.nf`, line 38, change:
+
+```groovy
+    ch_searchdb = channel.fromPath(params.database, checkIfExists: true).first()
+```
+
+To:
+
+```groovy
+    ch_searchdb = channel.fromPath(params.database, checkIfExists: true)
+        .ifEmpty { error("No protein database found at '${params.database}'. Provide --database <path/to/proteins.fasta>") }
+        .first()
+```
+
+- [ ] **Step 2: Guard ch_experiment_meta with ifEmpty**
+
+In `workflows/dia.nf`, line 46, change:
+
+```groovy
+    ch_experiment_meta = ch_result.meta.unique { m -> m.experiment_id }.first()
+```
+
+To:
+
+```groovy
+    ch_experiment_meta = ch_result.meta.unique { m -> m.experiment_id }
+        .ifEmpty { error("No valid input files found after SDRF parsing. Check your SDRF file and input paths.") }
+        .first()
+```
+
+- [ ] **Step 3: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+git add workflows/dia.nf
+git commit -m "fix: add empty input guards to prevent silent pipeline hangs
+
+Guard ch_searchdb and ch_experiment_meta with ifEmpty to fail fast
+with clear error messages instead of hanging indefinitely."
+```
+
+---
+
+## Task 4: Add DIA-NN 2.3.2 version config and profile
+
+**Files:**
+- Create: `conf/diann_versions/v2_3_2.config`
+- Modify: `nextflow.config:245-247` (profiles section)
+
+- [ ] **Step 1: Create v2_3_2.config**
+
+Create `conf/diann_versions/v2_3_2.config`:
+
+```groovy
+/*
+ * DIA-NN 2.3.2 container override (private ghcr.io)
+ * Latest release with DDA support and InfinDIA.
+ */
+params.diann_version = '2.3.2'
+
+process {
+    withLabel: diann {
+        container = 'ghcr.io/bigbio/diann:2.3.2'
+    }
+}
+
+singularity.enabled = false
+docker.enabled = true
+```
+
+- [ ] **Step 2: Add profile to nextflow.config**
+
+In `nextflow.config`, after the `diann_v2_2_0` profile line (around line 247), add:
+
+```groovy
+    diann_v2_3_2        { includeConfig 'conf/diann_versions/v2_3_2.config'    }
+```
+
+- [ ] **Step 3: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+git add conf/diann_versions/v2_3_2.config nextflow.config
+git commit -m "feat: add DIA-NN 2.3.2 version config and profile
+
+Adds conf/diann_versions/v2_3_2.config with ghcr.io/bigbio/diann:2.3.2
+container. Use -profile diann_v2_3_2 to opt in. Default stays 1.8.1.
+Enables DDA support and InfinDIA features."
+```
+
+---
+
+## Task 5: Implement DDA support — params, version guard, flag passthrough
+
+**Files:**
+- Modify: `nextflow.config:53-57` (DIA-NN general params)
+- Modify: `nextflow_schema.json` (DIA-NN section)
+- Modify: `workflows/dia.nf:35-38` (version guard)
+- Modify: `subworkflows/local/create_input_channel/main.nf:75-88` (acquisition method)
+- Modify: `modules/local/diann/insilico_library_generation/main.nf` (blocked list + flag)
+- Modify: `modules/local/diann/preliminary_analysis/main.nf` (blocked list + flag)
+- Modify: `modules/local/diann/assemble_empirical_library/main.nf` (blocked list + flag)
+- Modify: `modules/local/diann/individual_analysis/main.nf` (blocked list + flag)
+- Modify: `modules/local/diann/final_quantification/main.nf` (blocked list + flag)
+
+- [ ] **Step 1: Add diann_dda param to nextflow.config**
+
+In `nextflow.config`, after `diann_extra_args = null` (line 57), add:
+
+```groovy
+    diann_dda               = false  // Enable DDA analysis mode (requires DIA-NN >= 2.3.2)
+```
+
+- [ ] **Step 2: Add diann_dda to nextflow_schema.json**
+
+In `nextflow_schema.json`, in the DIA-NN section (inside `"$defs"` > appropriate group), add:
+
+```json
+"diann_dda": {
+    "type": "boolean",
+    "description": "Enable DDA (Data-Dependent Acquisition) analysis mode. Passes --dda to all DIA-NN steps. Requires DIA-NN >= 2.3.2 (use -profile diann_v2_3_2). Beta feature — only trust q-values, PEP, RT/IM, Ms1.Apex.Area. PTM localization unreliable with DDA.",
+    "fa_icon": "fas fa-flask",
+    "default": false
+}
+```
+
+Add `"diann_dda"` to the corresponding `"required"` or `"properties"` list in the appropriate group.
+
+- [ ] **Step 3: Add version guard in workflows/dia.nf**
+
+In `workflows/dia.nf`, at the start of the `main:` block (after line 37), add:
+
+```groovy
+    // Version guard for DDA mode
+    if (params.diann_dda && params.diann_version < '2.3.2') {
+        error("DDA mode (--diann_dda) requires DIA-NN >= 2.3.2. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
+    }
+```
+
+- [ ] **Step 4: Accept DDA acquisition method in create_input_channel**
+
+In `subworkflows/local/create_input_channel/main.nf`, replace lines 75-88 (the acquisition method validation block):
+
+```groovy
+    // Validate acquisition method
+    def acqMethod = row.AcquisitionMethod?.toString()?.trim() ?: ""
+    if (acqMethod.toLowerCase().contains("data-independent acquisition") || acqMethod.toLowerCase().contains("dia")) {
+        meta.acquisition_method = "dia"
+    } else if (params.diann_dda && (acqMethod.toLowerCase().contains("data-dependent acquisition") || acqMethod.toLowerCase().contains("dda"))) {
+        meta.acquisition_method = "dda"
+    } else if (acqMethod.isEmpty()) {
+        meta.acquisition_method = params.diann_dda ? "dda" : "dia"
+    } else {
+        log.error("Unsupported acquisition method: '${acqMethod}'. This pipeline supports DIA" + (params.diann_dda ? " and DDA (--diann_dda)" : "") + ". Found in file: ${filestr}")
+        exit(1)
+    }
+```
+
+- [ ] **Step 5: Add --dda flag to all 5 DIA-NN modules**
+
+For each of the 5 DIA-NN modules, make two changes:
+
+**a) Add `'--dda'` to the blocked list.** In each module's `def blocked = [...]`, add `'--dda'` to the array.
+
+**b) Add the flag variable and append it to the command.** In each module's script block, after the existing flag variables (before the `"""` shell block), add:
+
+```groovy
+    diann_dda_flag = params.diann_dda ? "--dda" : ""
+```
+
+Then append `${diann_dda_flag} \\` to the DIA-NN command, before `\${mod_flags}` (or before `$args` if no mod_flags).
+
+Apply to:
+- `modules/local/diann/insilico_library_generation/main.nf`
+- `modules/local/diann/preliminary_analysis/main.nf`
+- `modules/local/diann/assemble_empirical_library/main.nf`
+- `modules/local/diann/individual_analysis/main.nf`
+- `modules/local/diann/final_quantification/main.nf`
+
+- [ ] **Step 6: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+conda run -n nfcore nf-core pipelines lint --dir .
+git add nextflow.config nextflow_schema.json workflows/dia.nf subworkflows/local/create_input_channel/main.nf modules/local/diann/*/main.nf
+git commit -m "feat: add DDA support via --diann_dda flag (#5)
+
+- New param diann_dda (boolean, default: false)
+- Version guard: requires DIA-NN >= 2.3.2
+- Passes --dda to all 5 DIA-NN modules when enabled
+- Accepts DDA acquisition method in SDRF when diann_dda=true
+- Added --dda to blocked lists in all modules
+
+Closes #5"
+```
+
+---
+
+## Task 6: Add DDA test config
+
+**Files:**
+- Create: `conf/tests/test_dda.config`
+- Modify: `.github/workflows/extended_ci.yml:110-191` (stage 2a)
+
+- [ ] **Step 1: Create test_dda.config**
+
+Create `conf/tests/test_dda.config`:
+
+```groovy
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for testing DDA analysis (requires DIA-NN >= 2.3.2)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Tests DDA mode using the BSA dataset with --diann_dda flag.
+    Uses ghcr.io/bigbio/diann:2.3.2.
+
+    Use as follows:
+        nextflow run bigbio/quantmsdiann -profile test_dda,docker [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '12.GB',
+        time: '48.h'
+    ]
+}
+
+params {
+    config_profile_name        = 'Test profile for DDA analysis'
+    config_profile_description = 'DDA test using BSA dataset with DIA-NN 2.3.2.'
+
+    outdir = './results_dda'
+
+    // Input data — BSA DDA dataset
+    input = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/lfq_ci/BSA/BSA_design.sdrf.tsv'
+    database = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/lfq_ci/BSA/18Protein_SoCe_Tr_detergents_trace.fasta'
+
+    // DDA mode
+    diann_dda = true
+
+    // Search parameters matching BSA dataset
+    min_peptide_length = 7
+    max_peptide_length = 30
+    max_precursor_charge = 3
+    allowed_missed_cleavages = 1
+    diann_normalize = false
+    publish_dir_mode = 'symlink'
+    max_mods = 2
+}
+
+process {
+    withLabel: diann {
+        container = 'ghcr.io/bigbio/diann:2.3.2'
+    }
+}
+
+singularity.enabled = false
+docker.enabled = true
+```
+
+- [ ] **Step 2: Add test_dda profile to nextflow.config**
+
+In `nextflow.config`, after the `test_dia_2_2_0` profile line (around line 241), add:
+
+```groovy
+    test_dda            { includeConfig 'conf/tests/test_dda.config'           }
+```
+
+- [ ] **Step 3: Add test_dda to extended_ci.yml stage 2a**
+
+In `.github/workflows/extended_ci.yml`, in the `test-latest` job matrix (around line 120), add `"test_dda"` to the `test_profile` array:
+
+```yaml
+        test_profile: ["test_latest_dia", "test_dia_quantums", "test_dia_parquet", "test_dda"]
+```
+
+- [ ] **Step 4: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+git add conf/tests/test_dda.config nextflow.config .github/workflows/extended_ci.yml
+git commit -m "test: add DDA test config using BSA dataset with DIA-NN 2.3.2
+
+Uses bigbio/quantms-test-datasets BSA LFQ dataset (~34 MB) with
+diann_dda=true pinned to ghcr.io/bigbio/diann:2.3.2. Added to
+extended_ci.yml stage 2a (private containers)."
+```
+
+---
+
+## Task 7: Add test configs for skip_preliminary_analysis and speclib input
+
+**Files:**
+- Create: `conf/tests/test_dia_skip_preanalysis.config`
+- Modify: `nextflow.config` (profiles section)
+- Modify: `.github/workflows/extended_ci.yml` (stage 2a)
+
+- [ ] **Step 1: Create test_dia_skip_preanalysis.config**
+
+Create `conf/tests/test_dia_skip_preanalysis.config`:
+
+```groovy
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for testing skip_preliminary_analysis path
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Tests the pipeline with skip_preliminary_analysis=true, using default
+    mass accuracy parameters. Validates the untested code path in dia.nf.
+
+    Use as follows:
+        nextflow run bigbio/quantmsdiann -profile test_dia_skip_preanalysis,docker [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '12.GB',
+        time: '48.h'
+    ]
+}
+
+params {
+    config_profile_name        = 'Test profile for skip preliminary analysis'
+    config_profile_description = 'Tests skip_preliminary_analysis path with default mass accuracy params.'
+
+    outdir = './results_skip_preanalysis'
+
+    // Input data — same as test_dia
+    input = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/dia_ci/PXD026600.sdrf.tsv'
+    database = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/dia_ci/REF_EColi_K12_UPS1_combined.fasta'
+    min_pr_mz = 350
+    max_pr_mz = 950
+    min_fr_mz = 500
+    max_fr_mz = 1500
+    min_peptide_length = 15
+    max_peptide_length = 30
+    max_precursor_charge = 3
+    allowed_missed_cleavages = 1
+    diann_normalize = false
+    publish_dir_mode = 'symlink'
+    max_mods = 2
+
+    // Skip preliminary analysis — use default mass accuracy params
+    skip_preliminary_analysis = true
+    mass_acc_ms2 = 15
+    mass_acc_ms1 = 15
+    scan_window = 8
+}
+```
+
+- [ ] **Step 2: Add profile to nextflow.config**
+
+After existing test profiles (around line 242), add:
+
+```groovy
+    test_dia_skip_preanalysis { includeConfig 'conf/tests/test_dia_skip_preanalysis.config' }
+```
+
+- [ ] **Step 3: Add to extended_ci.yml stage 2a**
+
+In the `test-latest` job matrix, add `"test_dia_skip_preanalysis"` to the `test_profile` array.
+
+- [ ] **Step 4: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+git add conf/tests/test_dia_skip_preanalysis.config nextflow.config .github/workflows/extended_ci.yml
+git commit -m "test: add test config for skip_preliminary_analysis path
+
+Tests the previously untested code path where preliminary analysis is
+skipped and default mass accuracy parameters are used directly."
+```
+
+---
+
+## Task 8: Add new DIA-NN feature parameters (light-models, export-quant, site-ms1-quant)
+
+**Files:**
+- Modify: `nextflow.config` (params section)
+- Modify: `nextflow_schema.json`
+- Modify: `modules/local/diann/insilico_library_generation/main.nf` (light-models)
+- Modify: `modules/local/diann/final_quantification/main.nf` (export-quant, site-ms1-quant)
+
+- [ ] **Step 1: Add params to nextflow.config**
+
+In `nextflow.config`, in the DIA-NN general section (after `diann_dda`, around line 58), add:
+
+```groovy
+    diann_light_models      = false  // add '--light-models' for 10x faster library generation (DIA-NN >= 2.0)
+    diann_export_quant      = false  // add '--export-quant' for fragment-level parquet export (DIA-NN >= 2.0)
+    diann_site_ms1_quant    = false  // add '--site-ms1-quant' for MS1 apex PTM quantification (DIA-NN >= 2.0)
+```
+
+- [ ] **Step 2: Add params to nextflow_schema.json**
+
+Add each param to the DIA-NN section in the schema with type, description, default, and fa_icon.
+
+- [ ] **Step 3: Wire --light-models in insilico_library_generation**
+
+In `modules/local/diann/insilico_library_generation/main.nf`:
+
+a) Add `'--light-models'` to the blocked list (line 26-32).
+
+b) After `diann_no_peptidoforms` variable (line 47), add:
+
+```groovy
+    diann_light_models = params.diann_light_models ? "--light-models" : ""
+```
+
+c) Append `${diann_light_models} \\` to the DIA-NN command before `${met_excision}`.
+
+- [ ] **Step 4: Wire --export-quant and --site-ms1-quant in final_quantification**
+
+In `modules/local/diann/final_quantification/main.nf`:
+
+a) Add `'--export-quant'` and `'--site-ms1-quant'` to the blocked list (line 45-50).
+
+b) After `diann_dda_flag` variable, add:
+
+```groovy
+    diann_export_quant = params.diann_export_quant ? "--export-quant" : ""
+    diann_site_ms1_quant = params.diann_site_ms1_quant ? "--site-ms1-quant" : ""
+```
+
+c) Append both to the DIA-NN command before `\${mod_flags}`.
+
+- [ ] **Step 5: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+conda run -n nfcore nf-core pipelines lint --dir .
+git add nextflow.config nextflow_schema.json modules/local/diann/insilico_library_generation/main.nf modules/local/diann/final_quantification/main.nf
+git commit -m "feat: add --light-models, --export-quant, --site-ms1-quant params (#7)
+
+- diann_light_models: 10x faster in-silico library generation
+- diann_export_quant: fragment-level parquet export
+- diann_site_ms1_quant: MS1 apex intensities for PTM quantification
+All require DIA-NN >= 2.0."
+```
+
+---
+
+## Task 9: Add InfinDIA groundwork
+
+**Files:**
+- Modify: `nextflow.config` (params section)
+- Modify: `nextflow_schema.json`
+- Modify: `workflows/dia.nf` (version guard)
+- Modify: `modules/local/diann/insilico_library_generation/main.nf` (flag)
+
+- [ ] **Step 1: Add InfinDIA params to nextflow.config**
+
+After the DDA param, add:
+
+```groovy
+    // DIA-NN: InfinDIA (experimental, v2.3.0+)
+    enable_infin_dia        = false  // Enable InfinDIA for ultra-large search spaces
+    diann_pre_select        = null   // --pre-select N precursor limit for InfinDIA
+```
+
+- [ ] **Step 2: Add to nextflow_schema.json**
+
+Add `enable_infin_dia` (boolean) and `diann_pre_select` (integer, optional) to the schema.
+
+- [ ] **Step 3: Add version guard in workflows/dia.nf**
+
+After the DDA version guard, add:
+
+```groovy
+    if (params.enable_infin_dia && params.diann_version < '2.3.0') {
+        error("InfinDIA requires DIA-NN >= 2.3.0. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
+    }
+```
+
+- [ ] **Step 4: Wire flags in insilico_library_generation**
+
+In `modules/local/diann/insilico_library_generation/main.nf`:
+
+a) Add `'--infin-dia'` and `'--pre-select'` to the blocked list.
+
+b) Add flag variables:
+
+```groovy
+    infin_dia_flag = params.enable_infin_dia ? "--infin-dia" : ""
+    pre_select_flag = params.diann_pre_select ? "--pre-select $params.diann_pre_select" : ""
+```
+
+c) Append both to the DIA-NN command.
+
+- [ ] **Step 5: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+conda run -n nfcore nf-core pipelines lint --dir .
+git add nextflow.config nextflow_schema.json workflows/dia.nf modules/local/diann/insilico_library_generation/main.nf
+git commit -m "feat: add InfinDIA groundwork — enable_infin_dia param (#10)
+
+Experimental support for InfinDIA (DIA-NN 2.3.0+). Passes --infin-dia
+to library generation when enabled. Version guard enforces >= 2.3.0.
+No test config — InfinDIA requires large databases."
+```
+
+---
+
+## Task 10: Documentation — parameters.md
+
+**Files:**
+- Create: `docs/parameters.md`
+
+- [ ] **Step 1: Create comprehensive parameter reference**
+
+Create `docs/parameters.md` with all params from `nextflow_schema.json` grouped by category. Read `nextflow.config` and `nextflow_schema.json` to get every param, its type, default, and description. Group into:
+
+1. Input/output options
+2. File preparation
+3. DIA-NN general
+4. Mass accuracy and calibration
+5. Library generation
+6. Quantification and output
+7. DDA mode
+8. InfinDIA (experimental)
+9. Quality control
+10. MultiQC options
+11. Boilerplate
+
+Each param entry: `| name | type | default | description |`
+
+- [ ] **Step 2: Commit**
+
+```bash
+git add docs/parameters.md
+git commit -m "docs: add comprehensive parameter reference (#1)
+
+Complete reference for all ~70 pipeline parameters grouped by category
+with types, defaults, descriptions, and version requirements.
+
+Closes #1"
+```
+
+---
+
+## Task 11: Documentation — complete usage.md and output.md
+
+**Files:**
+- Modify: `docs/usage.md`
+- Modify: `docs/output.md`
+- Modify: `CITATIONS.md`
+- Modify: `README.md`
+
+- [ ] **Step 1: Add DDA section to usage.md**
+
+Add a "DDA Analysis Mode" section after the Bruker/timsTOF section with:
+- How to enable (`--diann_dda true -profile diann_v2_3_2`)
+- Limitations (beta, trusted columns only, PTM unreliable, MBR limited)
+- Example command
+- Link to DIA-NN DDA documentation
+
+- [ ] **Step 2: Add missing param sections to usage.md**
+
+Add sections for:
+- Preprocessing params (`reindex_mzml`, `mzml_statistics`, `convert_dotd`)
+- QC params (`enable_pmultiqc`, `skip_table_plots`, `contaminant_string`)
+- `diann_extra_args` scope per module
+- `--verbose_modules` profile
+- Container version override guide (DIA-NN version profiles)
+- Singularity usage
+- SLURM example
+
+- [ ] **Step 3: Update output.md**
+
+Add:
+- Parquet vs TSV output explanation
+- MSstats format section
+- Intermediate outputs under `--verbose_modules`
+
+- [ ] **Step 4: Add pmultiqc to CITATIONS.md**
+
+Add pmultiqc citation after the MultiQC entry.
+
+- [ ] **Step 5: Update README.md**
+
+Add DIA-NN version support table and link to `docs/parameters.md`.
+
+- [ ] **Step 6: Validate and commit**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+git add docs/usage.md docs/output.md CITATIONS.md README.md
+git commit -m "docs: complete usage.md, output.md, citations, README (#1, #3, #9, #15)
+
+- DDA mode documentation with limitations
+- Missing param sections (preprocessing, QC, extra_args scope)
+- Container version override and Singularity guides
+- Parquet vs TSV output explanation
+- pmultiqc citation added
+- README updated with version table
+
+Closes #3, #9, #15"
+```
+
+---
+
+## Task 12: Close resolved issues
+
+- [ ] **Step 1: Close issues via GitHub CLI**
+
+```bash
+gh issue close 17 --repo bigbio/quantmsdiann --comment "Already implemented — --monitor-mod is extracted from diann_config.cfg (generated by sdrf-pipelines convert-diann) and passed to all DIA-NN steps via mod_flags."
+gh issue close 2 --repo bigbio/quantmsdiann --comment "Superseded by #4 (Phase 6: consolidate param generation to sdrf-pipelines)."
+gh issue close 1 --repo bigbio/quantmsdiann --comment "Resolved — docs/parameters.md created with comprehensive parameter reference."
+gh issue close 3 --repo bigbio/quantmsdiann --comment "Resolved — diann_extra_args scope documented in docs/usage.md."
+gh issue close 9 --repo bigbio/quantmsdiann --comment "Resolved — container version override guide and Singularity usage added to docs/usage.md."
+gh issue close 15 --repo bigbio/quantmsdiann --comment "Resolved — docs/usage.md input documentation updated."
+```
+
+---
+
+## Task 13: Final validation and push
+
+- [ ] **Step 1: Run full validation suite**
+
+```bash
+conda run -n nfcore pre-commit run --all-files
+conda run -n nfcore nf-core pipelines lint --release --dir .
+```
+
+Expected: 0 failures on both.
+
+- [ ] **Step 2: Push dda branch and create PR**
+
+```bash
+git push -u origin dda
+gh pr create --title "feat: v1.0.0 release — robustness, DDA support, features, docs" --body "$(cat <<'PREOF'
+## Summary
+- Robustness fixes: pipefail, error_retry, empty input guards
+- DDA support via --diann_dda flag (DIA-NN >= 2.3.2)
+- New params: --light-models, --export-quant, --site-ms1-quant
+- InfinDIA groundwork (experimental)
+- DIA-NN 2.3.2 version config
+- New test configs: test_dda, test_dia_skip_preanalysis
+- Comprehensive docs: parameters.md, complete usage.md, output.md
+
+## Issues
+Closes #1, #3, #5, #7, #9, #10, #15, #17
+
+## Test plan
+- [ ] Existing CI tests pass (test_dia, test_dia_dotd)
+- [ ] New test_dda passes with BSA dataset on DIA-NN 2.3.2
+- [ ] test_dia_skip_preanalysis passes
+- [ ] nf-core lint --release: 0 failures
+- [ ] pre-commit: all passing
+PREOF
+)" --base dev
+```

From 7d4a441209de064827ea3c5d2148e2f00c5114e9 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:31:05 +0100
Subject: [PATCH 02/28] fix: add pipefail to all modules with tee pipes

Without pipefail, if the command before tee fails, tee returns 0 and
the Nextflow task appears to succeed. This masked failures in
generate_cfg, diann_msstats, samplesheet_check, and sdrf_parsing.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../2026-04-03-v1-release-implementation.md   | 22 +++++++-
 docs/v1-release-roadmap.md                    | 56 ++++++++++++-------
 modules/local/diann/diann_msstats/main.nf     |  1 +
 modules/local/diann/generate_cfg/main.nf      |  1 +
 modules/local/samplesheet_check/main.nf       |  1 +
 modules/local/sdrf_parsing/main.nf            |  1 +
 6 files changed, 59 insertions(+), 23 deletions(-)

diff --git a/docs/plans/2026-04-03-v1-release-implementation.md b/docs/plans/2026-04-03-v1-release-implementation.md
index 4b3d0ed..8439513 100644
--- a/docs/plans/2026-04-03-v1-release-implementation.md
+++ b/docs/plans/2026-04-03-v1-release-implementation.md
@@ -13,6 +13,7 @@
 ## Task 1: Fix tee pipes masking failures
 
 **Files:**
+
 - Modify: `modules/local/diann/generate_cfg/main.nf:26`
 - Modify: `modules/local/diann/diann_msstats/main.nf:21-26`
 - Modify: `modules/local/samplesheet_check/main.nf:38-43`
@@ -22,7 +23,7 @@
 
 In `modules/local/diann/generate_cfg/main.nf`, find the `"""` opening the script block (line 20) and add `set -o pipefail` as the first line:
 
-```groovy
+````groovy
     """
     set -o pipefail
     parse_sdrf generate-diann-cfg \\
@@ -71,13 +72,14 @@ git commit -m "fix: add pipefail to all modules with tee pipes
 Without pipefail, if the command before tee fails, tee returns 0 and
 the Nextflow task appears to succeed. This masked failures in
 generate_cfg, diann_msstats, samplesheet_check, and sdrf_parsing."
-```
+````
 
 ---
 
 ## Task 2: Add error retry to long-running DIA-NN tasks
 
 **Files:**
+
 - Modify: `modules/local/diann/preliminary_analysis/main.nf:3-4`
 - Modify: `modules/local/diann/individual_analysis/main.nf:3-4`
 - Modify: `modules/local/diann/final_quantification/main.nf:3-4`
@@ -102,6 +104,7 @@ Change to:
 ```
 
 Do the same for:
+
 - `individual_analysis/main.nf` (after `label 'diann'`)
 - `final_quantification/main.nf` (after `label 'diann'`)
 - `insilico_library_generation/main.nf` (after `label 'diann'`)
@@ -124,6 +127,7 @@ retry on signal exits (130-145, 104, 175)."
 ## Task 3: Add empty input guards
 
 **Files:**
+
 - Modify: `workflows/dia.nf:38,46`
 
 - [ ] **Step 1: Guard ch_searchdb with ifEmpty**
@@ -174,6 +178,7 @@ with clear error messages instead of hanging indefinitely."
 ## Task 4: Add DIA-NN 2.3.2 version config and profile
 
 **Files:**
+
 - Create: `conf/diann_versions/v2_3_2.config`
 - Modify: `nextflow.config:245-247` (profiles section)
 
@@ -223,6 +228,7 @@ Enables DDA support and InfinDIA features."
 ## Task 5: Implement DDA support — params, version guard, flag passthrough
 
 **Files:**
+
 - Modify: `nextflow.config:53-57` (DIA-NN general params)
 - Modify: `nextflow_schema.json` (DIA-NN section)
 - Modify: `workflows/dia.nf:35-38` (version guard)
@@ -301,6 +307,7 @@ For each of the 5 DIA-NN modules, make two changes:
 Then append `${diann_dda_flag} \\` to the DIA-NN command, before `\${mod_flags}` (or before `$args` if no mod_flags).
 
 Apply to:
+
 - `modules/local/diann/insilico_library_generation/main.nf`
 - `modules/local/diann/preliminary_analysis/main.nf`
 - `modules/local/diann/assemble_empirical_library/main.nf`
@@ -329,6 +336,7 @@ Closes #5"
 ## Task 6: Add DDA test config
 
 **Files:**
+
 - Create: `conf/tests/test_dda.config`
 - Modify: `.github/workflows/extended_ci.yml:110-191` (stage 2a)
 
@@ -404,7 +412,7 @@ In `nextflow.config`, after the `test_dia_2_2_0` profile line (around line 241),
 In `.github/workflows/extended_ci.yml`, in the `test-latest` job matrix (around line 120), add `"test_dda"` to the `test_profile` array:
 
 ```yaml
-        test_profile: ["test_latest_dia", "test_dia_quantums", "test_dia_parquet", "test_dda"]
+test_profile: ["test_latest_dia", "test_dia_quantums", "test_dia_parquet", "test_dda"]
 ```
 
 - [ ] **Step 4: Validate and commit**
@@ -424,6 +432,7 @@ extended_ci.yml stage 2a (private containers)."
 ## Task 7: Add test configs for skip_preliminary_analysis and speclib input
 
 **Files:**
+
 - Create: `conf/tests/test_dia_skip_preanalysis.config`
 - Modify: `nextflow.config` (profiles section)
 - Modify: `.github/workflows/extended_ci.yml` (stage 2a)
@@ -511,6 +520,7 @@ skipped and default mass accuracy parameters are used directly."
 ## Task 8: Add new DIA-NN feature parameters (light-models, export-quant, site-ms1-quant)
 
 **Files:**
+
 - Modify: `nextflow.config` (params section)
 - Modify: `nextflow_schema.json`
 - Modify: `modules/local/diann/insilico_library_generation/main.nf` (light-models)
@@ -578,6 +588,7 @@ All require DIA-NN >= 2.0."
 ## Task 9: Add InfinDIA groundwork
 
 **Files:**
+
 - Modify: `nextflow.config` (params section)
 - Modify: `nextflow_schema.json`
 - Modify: `workflows/dia.nf` (version guard)
@@ -640,6 +651,7 @@ No test config — InfinDIA requires large databases."
 ## Task 10: Documentation — parameters.md
 
 **Files:**
+
 - Create: `docs/parameters.md`
 
 - [ ] **Step 1: Create comprehensive parameter reference**
@@ -677,6 +689,7 @@ Closes #1"
 ## Task 11: Documentation — complete usage.md and output.md
 
 **Files:**
+
 - Modify: `docs/usage.md`
 - Modify: `docs/output.md`
 - Modify: `CITATIONS.md`
@@ -685,6 +698,7 @@ Closes #1"
 - [ ] **Step 1: Add DDA section to usage.md**
 
 Add a "DDA Analysis Mode" section after the Bruker/timsTOF section with:
+
 - How to enable (`--diann_dda true -profile diann_v2_3_2`)
 - Limitations (beta, trusted columns only, PTM unreliable, MBR limited)
 - Example command
@@ -693,6 +707,7 @@ Add a "DDA Analysis Mode" section after the Bruker/timsTOF section with:
 - [ ] **Step 2: Add missing param sections to usage.md**
 
 Add sections for:
+
 - Preprocessing params (`reindex_mzml`, `mzml_statistics`, `convert_dotd`)
 - QC params (`enable_pmultiqc`, `skip_table_plots`, `contaminant_string`)
 - `diann_extra_args` scope per module
@@ -704,6 +719,7 @@ Add sections for:
 - [ ] **Step 3: Update output.md**
 
 Add:
+
 - Parquet vs TSV output explanation
 - MSstats format section
 - Intermediate outputs under `--verbose_modules`
diff --git a/docs/v1-release-roadmap.md b/docs/v1-release-roadmap.md
index 421648f..1961f20 100644
--- a/docs/v1-release-roadmap.md
+++ b/docs/v1-release-roadmap.md
@@ -29,6 +29,7 @@ DDA parallelization is identical to DIA — per-file parallel for PRELIMINARY_AN
 ### 1.1 Fix tee pipes masking failures
 
 Add `set -o pipefail` or `exit ${PIPESTATUS[0]}` to script blocks in:
+
 - `modules/local/diann/generate_cfg/main.nf`
 - `modules/local/diann/diann_msstats/main.nf`
 - `modules/local/samplesheet_check/main.nf`
@@ -39,6 +40,7 @@ Add `set -o pipefail` or `exit ${PIPESTATUS[0]}` to script blocks in:
 ### 1.2 Add error retry to long-running DIA-NN tasks
 
 Add `label 'error_retry'` to:
+
 - PRELIMINARY_ANALYSIS (process_high)
 - INDIVIDUAL_ANALYSIS (process_high)
 - FINAL_QUANTIFICATION (process_high)
@@ -55,12 +57,14 @@ These are the longest-running tasks and most susceptible to transient failures (
 ### 1.4 New test configs
 
 **`conf/tests/test_dia_skip_preanalysis.config`:**
+
 - Sets `skip_preliminary_analysis = true`
 - Uses default `mass_acc_ms1`, `mass_acc_ms2`, `scan_window` params
 - Same PXD026600 test data as test_dia
 - Validates the skip path that is currently untested in CI
 
 **`conf/tests/test_dia_speclib.config`:**
+
 - Sets `diann_speclib` to a pre-built spectral library
 - Skips INSILICO_LIBRARY_GENERATION (the `if` branch in dia.nf line 55-56)
 - Requires a small test spectral library in quantms-test-datasets (or generated from existing test data)
@@ -78,6 +82,7 @@ Build and push `ghcr.io/bigbio/diann:2.3.2` from existing Dockerfile at `quantms
 ### 2.2 Version config
 
 Add `conf/diann_versions/v2_3_2.config`:
+
 ```groovy
 params.diann_version = '2.3.2'
 process {
@@ -90,6 +95,7 @@ docker.enabled = true
 ```
 
 Add profile in `nextflow.config`:
+
 ```groovy
 diann_v2_3_2 { includeConfig 'conf/diann_versions/v2_3_2.config' }
 ```
@@ -97,11 +103,13 @@ diann_v2_3_2 { includeConfig 'conf/diann_versions/v2_3_2.config' }
 ### 2.3 DDA implementation
 
 **New param** in `nextflow.config`:
+
 ```groovy
 diann_dda = false  // Enable DDA analysis mode (requires DIA-NN >= 2.3.2)
 ```
 
 **Version guard** in `workflows/dia.nf` at workflow start:
+
 ```groovy
 if (params.diann_dda && params.diann_version < '2.3.2') {
     error("DDA mode requires DIA-NN >= 2.3.2. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
@@ -109,12 +117,15 @@ if (params.diann_dda && params.diann_version < '2.3.2') {
 ```
 
 **Pass `--dda` to all DIA-NN modules** — In each module's script block, add:
+
 ```groovy
 diann_dda_flag = params.diann_dda ? "--dda" : ""
 ```
+
 And append `${diann_dda_flag}` to the DIA-NN command. Add `'--dda'` to the `blocked` list in all 5 modules.
 
 **Accept DDA in create_input_channel** — Modify `create_input_channel/main.nf` lines 78-88:
+
 ```groovy
 if (acqMethod.toLowerCase().contains("data-independent acquisition") || acqMethod.toLowerCase().contains("dia")) {
     meta.acquisition_method = "dia"
@@ -135,6 +146,7 @@ Add `comment[proteomics data acquisition method]` column with value `NT=Data-Dep
 ### 2.5 Test config
 
 **`conf/tests/test_dda.config`:**
+
 - Points to BSA dataset from `bigbio/quantms-test-datasets/testdata/lfq_ci/BSA/`
 - Sets `diann_dda = true`
 - Pins to `ghcr.io/bigbio/diann:2.3.2`
@@ -151,22 +163,24 @@ Add `comment[proteomics data acquisition method]` column with value `NT=Data-Dep
 
 ### 3.1 New DIA-NN parameters
 
-| Parameter | Flag | Min Version | Module | Default |
-|---|---|---|---|---|
-| `diann_light_models` | `--light-models` | 2.0 | INSILICO_LIBRARY_GENERATION | false |
-| `diann_export_quant` | `--export-quant` | 2.0 | FINAL_QUANTIFICATION | false |
-| `diann_read_threads` | `--read-threads N` | 2.0 | All DIA-NN steps | null (disabled) |
-| `diann_site_ms1_quant` | `--site-ms1-quant` | 2.0 | FINAL_QUANTIFICATION | false |
+| Parameter              | Flag               | Min Version | Module                      | Default         |
+| ---------------------- | ------------------ | ----------- | --------------------------- | --------------- |
+| `diann_light_models`   | `--light-models`   | 2.0         | INSILICO_LIBRARY_GENERATION | false           |
+| `diann_export_quant`   | `--export-quant`   | 2.0         | FINAL_QUANTIFICATION        | false           |
+| `diann_read_threads`   | `--read-threads N` | 2.0         | All DIA-NN steps            | null (disabled) |
+| `diann_site_ms1_quant` | `--site-ms1-quant` | 2.0         | FINAL_QUANTIFICATION        | false           |
 
 Each parameter: add to `nextflow.config`, `nextflow_schema.json`, module script block (with version guard where needed), and module blocked list.
 
 ### 3.2 InfinDIA groundwork (issue #10)
 
 New params:
+
 - `enable_infin_dia` (boolean, default: false) — requires >= 2.3.0
 - `diann_pre_select` (integer, optional) — `--pre-select N` precursor limit
 
 Implementation:
+
 - Pass `--infin-dia` to INSILICO_LIBRARY_GENERATION when enabled
 - Version guard: error if enabled with DIA-NN < 2.3.0
 - No test config — InfinDIA needs large databases to be meaningful
@@ -185,6 +199,7 @@ Implementation:
 ### 4.1 Create `docs/parameters.md`
 
 Comprehensive parameter reference with all ~70 params grouped by:
+
 - Input/output options
 - File preparation (conversion, indexing, statistics)
 - DIA-NN general settings
@@ -202,6 +217,7 @@ Each param: name, type, default, description, version requirement (if any).
 ### 4.2 Complete `docs/usage.md`
 
 Add missing sections:
+
 - Preprocessing params (`reindex_mzml`, `mzml_statistics`, `convert_dotd`)
 - QC params (`enable_pmultiqc`, `skip_table_plots`, `contaminant_string`)
 - MultiQC options
@@ -231,20 +247,20 @@ Add missing sections:
 
 ## Issues Status After Release
 
-| Issue | Status | Resolution |
-|---|---|---|
-| #1 | Closed | Parameter documentation created |
-| #2 | Closed | Superseded by #4 |
-| #3 | Closed | ext.args scope documented |
-| #5 | Closed | DDA support implemented |
-| #7 | Closed | Phase 2 features wired |
-| #9 | Closed | Container docs added |
-| #10 | Partially closed | InfinDIA groundwork done, full support needs testing |
-| #15 | Closed | Docs mismatch fixed |
-| #17 | Closed | Already implemented |
-| #4 | Open | Blocked on sdrf-pipelines converter release |
-| #6 | Open | Blocked on PRIDE ontology release |
-| #25 | Open | QPX deferred to next release |
+| Issue | Status           | Resolution                                           |
+| ----- | ---------------- | ---------------------------------------------------- |
+| #1    | Closed           | Parameter documentation created                      |
+| #2    | Closed           | Superseded by #4                                     |
+| #3    | Closed           | ext.args scope documented                            |
+| #5    | Closed           | DDA support implemented                              |
+| #7    | Closed           | Phase 2 features wired                               |
+| #9    | Closed           | Container docs added                                 |
+| #10   | Partially closed | InfinDIA groundwork done, full support needs testing |
+| #15   | Closed           | Docs mismatch fixed                                  |
+| #17   | Closed           | Already implemented                                  |
+| #4    | Open             | Blocked on sdrf-pipelines converter release          |
+| #6    | Open             | Blocked on PRIDE ontology release                    |
+| #25   | Open             | QPX deferred to next release                         |
 
 ---
 
diff --git a/modules/local/diann/diann_msstats/main.nf b/modules/local/diann/diann_msstats/main.nf
index 4374b58..1844fdc 100644
--- a/modules/local/diann/diann_msstats/main.nf
+++ b/modules/local/diann/diann_msstats/main.nf
@@ -18,6 +18,7 @@ process DIANN_MSSTATS {
     script:
     def args = task.ext.args ?: ''
     """
+    set -o pipefail
     quantmsutilsc diann2msstats \\
         --report ${report} \\
         --exp_design ${exp_design} \\
diff --git a/modules/local/diann/generate_cfg/main.nf b/modules/local/diann/generate_cfg/main.nf
index 8377030..8e36641 100644
--- a/modules/local/diann/generate_cfg/main.nf
+++ b/modules/local/diann/generate_cfg/main.nf
@@ -18,6 +18,7 @@ process GENERATE_CFG {
     def args = task.ext.args ?: ''
 
     """
+    set -o pipefail
     quantmsutilsc dianncfg \\
         --enzyme "${meta.enzyme}" \\
         --fix_mod "${meta.fixedmodifications}" \\
diff --git a/modules/local/samplesheet_check/main.nf b/modules/local/samplesheet_check/main.nf
index f2b7112..76fae90 100644
--- a/modules/local/samplesheet_check/main.nf
+++ b/modules/local/samplesheet_check/main.nf
@@ -23,6 +23,7 @@ process SAMPLESHEET_CHECK {
     def string_use_ols_cache_only = params.use_ols_cache_only == true ? "--use_ols_cache_only" : ""
 
     """
+    set -o pipefail
     # Get basename and create output filename
     BASENAME=\$(basename "${input_file}")
     # Remove .sdrf.tsv, .sdrf.csv, or .sdrf extension (in that order to match longest first)
diff --git a/modules/local/sdrf_parsing/main.nf b/modules/local/sdrf_parsing/main.nf
index a89bc61..61803f3 100644
--- a/modules/local/sdrf_parsing/main.nf
+++ b/modules/local/sdrf_parsing/main.nf
@@ -22,6 +22,7 @@ process SDRF_PARSING {
     def diann_version_flag = params.diann_version ? "--diann_version '${params.diann_version}'" : ''
 
     """
+    set -o pipefail
     parse_sdrf convert-diann \\
         -s ${sdrf} \\
         ${mod_loc_flag} \\

From 853dbbf6000cd4fe8195ca94cf03a3188a07d4ab Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:32:22 +0100
Subject: [PATCH 03/28] fix: add error_retry label to all DIA-NN analysis
 modules

These are the longest-running tasks and most susceptible to transient
failures (OOM, I/O timeouts). The error_retry label enables automatic
retry on signal exits (130-145, 104, 175).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 modules/local/diann/assemble_empirical_library/main.nf  | 1 +
 modules/local/diann/final_quantification/main.nf        | 1 +
 modules/local/diann/individual_analysis/main.nf         | 1 +
 modules/local/diann/insilico_library_generation/main.nf | 1 +
 modules/local/diann/preliminary_analysis/main.nf        | 1 +
 5 files changed, 5 insertions(+)

diff --git a/modules/local/diann/assemble_empirical_library/main.nf b/modules/local/diann/assemble_empirical_library/main.nf
index 034b95e..6efde30 100644
--- a/modules/local/diann/assemble_empirical_library/main.nf
+++ b/modules/local/diann/assemble_empirical_library/main.nf
@@ -2,6 +2,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
     tag "$meta.experiment_id"
     label 'process_low'
     label 'diann'
+    label 'error_retry'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
diff --git a/modules/local/diann/final_quantification/main.nf b/modules/local/diann/final_quantification/main.nf
index defb66d..42a0a6f 100644
--- a/modules/local/diann/final_quantification/main.nf
+++ b/modules/local/diann/final_quantification/main.nf
@@ -2,6 +2,7 @@ process FINAL_QUANTIFICATION {
     tag "$meta.experiment_id"
     label 'process_high'
     label 'diann'
+    label 'error_retry'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
diff --git a/modules/local/diann/individual_analysis/main.nf b/modules/local/diann/individual_analysis/main.nf
index 28cb3b5..4a11628 100644
--- a/modules/local/diann/individual_analysis/main.nf
+++ b/modules/local/diann/individual_analysis/main.nf
@@ -2,6 +2,7 @@ process INDIVIDUAL_ANALYSIS {
     tag "$ms_file.baseName"
     label 'process_high'
     label 'diann'
+    label 'error_retry'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
diff --git a/modules/local/diann/insilico_library_generation/main.nf b/modules/local/diann/insilico_library_generation/main.nf
index b347483..a26d9c6 100644
--- a/modules/local/diann/insilico_library_generation/main.nf
+++ b/modules/local/diann/insilico_library_generation/main.nf
@@ -2,6 +2,7 @@ process INSILICO_LIBRARY_GENERATION {
     tag "$fasta.name"
     label 'process_medium'
     label 'diann'
+    label 'error_retry'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :
diff --git a/modules/local/diann/preliminary_analysis/main.nf b/modules/local/diann/preliminary_analysis/main.nf
index 925114e..df88586 100644
--- a/modules/local/diann/preliminary_analysis/main.nf
+++ b/modules/local/diann/preliminary_analysis/main.nf
@@ -2,6 +2,7 @@ process PRELIMINARY_ANALYSIS {
     tag "$ms_file.baseName"
     label 'process_high'
     label 'diann'
+    label 'error_retry'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://containers.biocontainers.pro/s3/SingImgsRepo/diann/v1.8.1_cv1/diann_v1.8.1_cv1.img' :

From d85847ecee9f86905396f6cc48deea4a2bf596e7 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:33:21 +0100
Subject: [PATCH 04/28] fix: add empty input guards to prevent silent pipeline
 hangs

Guard ch_searchdb and ch_experiment_meta with ifEmpty to fail fast
with clear error messages instead of hanging indefinitely.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 workflows/dia.nf | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/workflows/dia.nf b/workflows/dia.nf
index d693a10..dabbb74 100644
--- a/workflows/dia.nf
+++ b/workflows/dia.nf
@@ -35,7 +35,9 @@ workflow DIA {
     main:
 
     ch_software_versions = channel.empty()
-    ch_searchdb = channel.fromPath(params.database, checkIfExists: true).first()
+    ch_searchdb = channel.fromPath(params.database, checkIfExists: true)
+        .ifEmpty { error("No protein database found at '${params.database}'. Provide --database <path/to/proteins.fasta>") }
+        .first()
 
     ch_file_preparation_results.multiMap {
         result ->
@@ -43,7 +45,9 @@ workflow DIA {
         ms_file:result[1]
     }.set { ch_result }
 
-    ch_experiment_meta = ch_result.meta.unique { m -> m.experiment_id }.first()
+    ch_experiment_meta = ch_result.meta.unique { m -> m.experiment_id }
+        .ifEmpty { error("No valid input files found after SDRF parsing. Check your SDRF file and input paths.") }
+        .first()
 
     // diann_config.cfg comes directly from SDRF_PARSING (convert-diann)
     // Convert to value channel so it can be consumed by all per-file processes

From f2a6777c8764ae1f73bb3a1c307f68df64a20b77 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:34:28 +0100
Subject: [PATCH 05/28] feat: add DIA-NN 2.3.2 version config and profile

Adds conf/diann_versions/v2_3_2.config with ghcr.io/bigbio/diann:2.3.2
container. Use -profile diann_v2_3_2 to opt in. Default stays 1.8.1.
Enables DDA support and InfinDIA features.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 conf/diann_versions/v2_3_2.config | 14 ++++++++++++++
 nextflow.config                   |  1 +
 2 files changed, 15 insertions(+)
 create mode 100644 conf/diann_versions/v2_3_2.config

diff --git a/conf/diann_versions/v2_3_2.config b/conf/diann_versions/v2_3_2.config
new file mode 100644
index 0000000..2912f15
--- /dev/null
+++ b/conf/diann_versions/v2_3_2.config
@@ -0,0 +1,14 @@
+/*
+ * DIA-NN 2.3.2 container override (private ghcr.io)
+ * Latest release with DDA support and InfinDIA.
+ */
+params.diann_version = '2.3.2'
+
+process {
+    withLabel: diann {
+        container = 'ghcr.io/bigbio/diann:2.3.2'
+    }
+}
+
+singularity.enabled = false
+docker.enabled = true
diff --git a/nextflow.config b/nextflow.config
index 88c8c88..8ed056a 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -245,6 +245,7 @@ profiles {
     diann_v1_8_1        { includeConfig 'conf/diann_versions/v1_8_1.config'    }
     diann_v2_1_0        { includeConfig 'conf/diann_versions/v2_1_0.config'    }
     diann_v2_2_0        { includeConfig 'conf/diann_versions/v2_2_0.config'    }
+    diann_v2_3_2        { includeConfig 'conf/diann_versions/v2_3_2.config'    }
     dev             { includeConfig 'conf/dev.config'                   }
     pride_slurm     { includeConfig 'conf/pride_codon_slurm.config'     }
     manual_wave     { includeConfig 'conf/wave.config'                  }

From 14ed74831132c0b0ae426223e409f057e5ddcf58 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:40:19 +0100
Subject: [PATCH 06/28] feat: add DDA support via --diann_dda flag (#5)

- New param diann_dda (boolean, default: false)
- Version guard: requires DIA-NN >= 2.3.2
- Passes --dda to all 5 DIA-NN modules when enabled
- Accepts DDA acquisition method in SDRF when diann_dda=true
- Added --dda to blocked lists in all modules

Closes #5

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 modules.json                                     |  2 +-
 .../diann/assemble_empirical_library/main.nf     |  4 +++-
 modules/local/diann/final_quantification/main.nf |  4 +++-
 modules/local/diann/individual_analysis/main.nf  |  4 +++-
 .../diann/insilico_library_generation/main.nf    |  4 +++-
 modules/local/diann/preliminary_analysis/main.nf |  4 +++-
 nextflow.config                                  |  1 +
 nextflow_schema.json                             |  6 ++++++
 subworkflows/local/create_input_channel/main.nf  | 16 +++++++---------
 workflows/dia.nf                                 |  6 ++++++
 10 files changed, 36 insertions(+), 15 deletions(-)

diff --git a/modules.json b/modules.json
index c0e263c..be82844 100644
--- a/modules.json
+++ b/modules.json
@@ -46,4 +46,4 @@
             }
         }
     }
-}
+}
\ No newline at end of file
diff --git a/modules/local/diann/assemble_empirical_library/main.nf b/modules/local/diann/assemble_empirical_library/main.nf
index 6efde30..de7a9e4 100644
--- a/modules/local/diann/assemble_empirical_library/main.nf
+++ b/modules/local/diann/assemble_empirical_library/main.nf
@@ -32,7 +32,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
          '--mass-acc', '--mass-acc-ms1', '--window',
          '--individual-mass-acc', '--individual-windows',
          '--out-lib', '--use-quant', '--gen-spec-lib', '--rt-profiling',
-         '--monitor-mod', '--var-mod', '--fixed-mod']
+         '--monitor-mod', '--var-mod', '--fixed-mod', '--dda']
     // Sort by length descending so longer flags (e.g. --mass-acc-ms1) are matched before shorter prefixes (--mass-acc)
     blocked.sort { a -> -a.length() }.each { flag ->
         def flagPattern = '(?<=^|\\s)' + java.util.regex.Pattern.quote(flag) + '(?=\\s|\$)(\\s+(?!-{1,2}[a-zA-Z])\\S+)*'
@@ -53,6 +53,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
     diann_tims_sum = params.diann_tims_sum ? "--quant-tims-sum" : ""
     diann_im_window = params.diann_im_window ? "--im-window $params.diann_im_window" : ""
+    diann_dda_flag = params.diann_dda ? "--dda" : ""
 
     """
     # Precursor Tolerance value was: ${meta['precursormasstolerance']}
@@ -79,6 +80,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
             ${diann_no_peptidoforms} \\
             ${diann_tims_sum} \\
             ${diann_im_window} \\
+            ${diann_dda_flag} \\
             \${mod_flags} \\
             $args
 
diff --git a/modules/local/diann/final_quantification/main.nf b/modules/local/diann/final_quantification/main.nf
index 42a0a6f..8e6c76d 100644
--- a/modules/local/diann/final_quantification/main.nf
+++ b/modules/local/diann/final_quantification/main.nf
@@ -48,7 +48,7 @@ process FINAL_QUANTIFICATION {
          '--use-quant', '--matrices', '--out', '--relaxed-prot-inf', '--pg-level',
          '--qvalue', '--window', '--individual-windows',
          '--species-genes', '--report-decoys', '--xic', '--no-norm',
-         '--monitor-mod', '--var-mod', '--fixed-mod']
+         '--monitor-mod', '--var-mod', '--fixed-mod', '--dda']
     // Sort by length descending so longer flags (e.g. --individual-windows) are matched before shorter prefixes (--window)
     blocked.sort { a -> -a.length() }.each { flag ->
         def flagPattern = '(?<=^|\\s)' + java.util.regex.Pattern.quote(flag) + '(?=\\s|\$)(\\s+(?!-{1,2}[a-zA-Z])\\S+)*'
@@ -69,6 +69,7 @@ process FINAL_QUANTIFICATION {
     quantums_params = params.quantums_params ? "--quant-params $params.quantums_params": ""
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
     diann_use_quant = params.diann_use_quant ? "--use-quant" : ""
+    diann_dda_flag = params.diann_dda ? "--dda" : ""
 
     """
     # Notes: if .quant files are passed, mzml/.d files are not accessed, so the name needs to be passed but files
@@ -98,6 +99,7 @@ process FINAL_QUANTIFICATION {
             ${quantums_params} \\
             ${diann_no_peptidoforms} \\
             ${diann_use_quant} \\
+            ${diann_dda_flag} \\
             \${mod_flags} \\
             $args
 
diff --git a/modules/local/diann/individual_analysis/main.nf b/modules/local/diann/individual_analysis/main.nf
index 4a11628..1e24905 100644
--- a/modules/local/diann/individual_analysis/main.nf
+++ b/modules/local/diann/individual_analysis/main.nf
@@ -28,7 +28,7 @@ process INDIVIDUAL_ANALYSIS {
          '--mass-acc', '--mass-acc-ms1', '--window',
          '--no-ifs-removal', '--no-main-report', '--relaxed-prot-inf', '--pg-level',
          '--min-pr-mz', '--max-pr-mz', '--min-fr-mz', '--max-fr-mz',
-         '--monitor-mod', '--var-mod', '--fixed-mod']
+         '--monitor-mod', '--var-mod', '--fixed-mod', '--dda']
     // Sort by length descending so longer flags (e.g. --mass-acc-ms1) are matched before shorter prefixes (--mass-acc)
     blocked.sort { a -> -a.length() }.each { flag ->
         def flagPattern = '(?<=^|\\s)' + java.util.regex.Pattern.quote(flag) + '(?=\\s|\$)(\\s+(?!-{1,2}[a-zA-Z])\\S+)*'
@@ -82,6 +82,7 @@ process INDIVIDUAL_ANALYSIS {
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
     diann_tims_sum = params.diann_tims_sum ? "--quant-tims-sum" : ""
     diann_im_window = params.diann_im_window ? "--im-window $params.diann_im_window" : ""
+    diann_dda_flag = params.diann_dda ? "--dda" : ""
 
     // Per-file scan ranges from SDRF (empty = no flag, DIA-NN auto-detects)
     min_pr_mz = meta['ms1minmz'] ? "--min-pr-mz ${meta['ms1minmz']}" : ""
@@ -113,6 +114,7 @@ process INDIVIDUAL_ANALYSIS {
             ${diann_no_peptidoforms} \\
             ${diann_tims_sum} \\
             ${diann_im_window} \\
+            ${diann_dda_flag} \\
             \${mod_flags} \\
             $args
 
diff --git a/modules/local/diann/insilico_library_generation/main.nf b/modules/local/diann/insilico_library_generation/main.nf
index a26d9c6..321cc2f 100644
--- a/modules/local/diann/insilico_library_generation/main.nf
+++ b/modules/local/diann/insilico_library_generation/main.nf
@@ -30,7 +30,7 @@ process INSILICO_LIBRARY_GENERATION {
          '--missed-cleavages', '--min-pep-len', '--max-pep-len',
          '--min-pr-charge', '--max-pr-charge', '--var-mods',
          '--min-pr-mz', '--max-pr-mz', '--min-fr-mz', '--max-fr-mz',
-         '--met-excision', '--monitor-mod']
+         '--met-excision', '--monitor-mod', '--dda']
     // Sort by length descending so longer flags (e.g. --fasta-search) are matched before shorter prefixes (--fasta, --f)
     blocked.sort { a -> -a.length() }.each { flag ->
         def flagPattern = '(?<=^|\\s)' + java.util.regex.Pattern.quote(flag) + '(?=\\s|\$)(\\s+(?!-{1,2}[a-zA-Z])\\S+)*'
@@ -46,6 +46,7 @@ process INSILICO_LIBRARY_GENERATION {
     max_fr_mz = params.max_fr_mz ? "--max-fr-mz $params.max_fr_mz":""
     met_excision = params.met_excision ? "--met-excision" : ""
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
+    diann_dda_flag = params.diann_dda ? "--dda" : ""
 
     """
     diann `cat ${diann_config}` \\
@@ -67,6 +68,7 @@ process INSILICO_LIBRARY_GENERATION {
             --gen-spec-lib \\
             ${diann_no_peptidoforms} \\
             ${met_excision} \\
+            ${diann_dda_flag} \\
             ${args}
 
     cp *lib.log.txt silicolibrarygeneration.log
diff --git a/modules/local/diann/preliminary_analysis/main.nf b/modules/local/diann/preliminary_analysis/main.nf
index df88586..791dab3 100644
--- a/modules/local/diann/preliminary_analysis/main.nf
+++ b/modules/local/diann/preliminary_analysis/main.nf
@@ -28,7 +28,7 @@ process PRELIMINARY_ANALYSIS {
          '--mass-acc', '--mass-acc-ms1', '--window',
          '--quick-mass-acc', '--min-corr', '--corr-diff', '--time-corr-only',
          '--min-pr-mz', '--max-pr-mz', '--min-fr-mz', '--max-fr-mz',
-         '--monitor-mod', '--var-mod', '--fixed-mod', '--no-prot-inf']
+         '--monitor-mod', '--var-mod', '--fixed-mod', '--no-prot-inf', '--dda']
     // Sort by length descending so longer flags (e.g. --mass-acc-ms1) are matched before shorter prefixes (--mass-acc)
     blocked.sort { a -> -a.length() }.each { flag ->
         def flagPattern = '(?<=^|\\s)' + java.util.regex.Pattern.quote(flag) + '(?=\\s|\$)(\\s+(?!-{1,2}[a-zA-Z])\\S+)*'
@@ -67,6 +67,7 @@ process PRELIMINARY_ANALYSIS {
     scan_window = params.scan_window_automatic ? '' : "--window $params.scan_window"
     diann_tims_sum = params.diann_tims_sum ? "--quant-tims-sum" : ""
     diann_im_window = params.diann_im_window ? "--im-window $params.diann_im_window" : ""
+    diann_dda_flag = params.diann_dda ? "--dda" : ""
 
     // Per-file scan ranges from SDRF (empty = no flag, DIA-NN auto-detects)
     min_pr_mz = meta['ms1minmz'] ? "--min-pr-mz ${meta['ms1minmz']}" : ""
@@ -102,6 +103,7 @@ process PRELIMINARY_ANALYSIS {
             ${diann_tims_sum} \\
             ${diann_im_window} \\
             --no-prot-inf \\
+            ${diann_dda_flag} \\
             \${mod_flags} \\
             $args
 
diff --git a/nextflow.config b/nextflow.config
index 8ed056a..3340937 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -55,6 +55,7 @@ params {
     diann_debug             = 3
     diann_speclib           = null
     diann_extra_args        = null
+    diann_dda               = false  // Enable DDA analysis mode (requires DIA-NN >= 2.3.2)
 
     // Optional outputs — control which intermediate files are published
     save_speclib_tsv        = false  // Save the TSV spectral library from in-silico generation
diff --git a/nextflow_schema.json b/nextflow_schema.json
index a4e288e..4a65114 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -469,6 +469,12 @@
                     "hidden": false,
                     "help_text": "Pass additional DIA-NN command-line arguments that will be appended to all DIA-NN steps (INSILICO_LIBRARY_GENERATION, PRELIMINARY_ANALYSIS, ASSEMBLE_EMPIRICAL_LIBRARY, INDIVIDUAL_ANALYSIS, FINAL_QUANTIFICATION). Flags that conflict with a specific step are automatically stripped with a warning. For step-specific overrides, use custom Nextflow config files with ext.args."
                 },
+                "diann_dda": {
+                    "type": "boolean",
+                    "description": "Enable DDA (Data-Dependent Acquisition) analysis mode. Passes --dda to all DIA-NN steps. Requires DIA-NN >= 2.3.2 (use -profile diann_v2_3_2). Beta feature.",
+                    "fa_icon": "fas fa-flask",
+                    "default": false
+                },
                 "save_speclib_tsv": {
                     "type": "boolean",
                     "default": false,
diff --git a/subworkflows/local/create_input_channel/main.nf b/subworkflows/local/create_input_channel/main.nf
index 588e144..c0249f1 100644
--- a/subworkflows/local/create_input_channel/main.nf
+++ b/subworkflows/local/create_input_channel/main.nf
@@ -72,18 +72,16 @@ def create_meta_channel(LinkedHashMap row, enzymes, files, wrapper) {
         exit(1, "ERROR: Please check input file -> File Uri does not exist!\n${filestr}")
     }
 
-    // Validate acquisition method is DIA
-    // AcquisitionMethod is already extracted by convert-diann (e.g. "Data-Independent Acquisition")
+    // Validate acquisition method
     def acqMethod = row.AcquisitionMethod?.toString()?.trim() ?: ""
     if (acqMethod.toLowerCase().contains("data-independent acquisition") || acqMethod.toLowerCase().contains("dia")) {
         meta.acquisition_method = "dia"
-    }
-    else if (acqMethod.isEmpty()) {
-        // If no acquisition method column in SDRF, assume DIA (this is a DIA-only pipeline)
-        meta.acquisition_method = "dia"
-    }
-    else {
-        log.error("This pipeline only supports Data-Independent Acquisition (DIA). Found: '${acqMethod}'. Use the quantms pipeline for DDA workflows.")
+    } else if (params.diann_dda && (acqMethod.toLowerCase().contains("data-dependent acquisition") || acqMethod.toLowerCase().contains("dda"))) {
+        meta.acquisition_method = "dda"
+    } else if (acqMethod.isEmpty()) {
+        meta.acquisition_method = params.diann_dda ? "dda" : "dia"
+    } else {
+        log.error("Unsupported acquisition method: '${acqMethod}'. This pipeline supports DIA" + (params.diann_dda ? " and DDA (--diann_dda)" : "") + ". Found in file: ${filestr}")
         exit(1)
     }
 
diff --git a/workflows/dia.nf b/workflows/dia.nf
index dabbb74..7041d80 100644
--- a/workflows/dia.nf
+++ b/workflows/dia.nf
@@ -35,6 +35,12 @@ workflow DIA {
     main:
 
     ch_software_versions = channel.empty()
+
+    // Version guard for DDA mode
+    if (params.diann_dda && params.diann_version < '2.3.2') {
+        error("DDA mode (--diann_dda) requires DIA-NN >= 2.3.2. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
+    }
+
     ch_searchdb = channel.fromPath(params.database, checkIfExists: true)
         .ifEmpty { error("No protein database found at '${params.database}'. Provide --database <path/to/proteins.fasta>") }
         .first()

From 7f51d00f3cabd13275e4ed3eaea7b238ef160273 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:42:13 +0100
Subject: [PATCH 07/28] test: add DDA and skip_preanalysis test configs

- test_dda: BSA dataset with diann_dda=true on DIA-NN 2.3.2
- test_dia_skip_preanalysis: tests previously untested skip path
Both added to extended_ci.yml stage 2a.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .github/workflows/extended_ci.yml           |  3 +-
 conf/tests/test_dda.config                  | 52 +++++++++++++++++++++
 conf/tests/test_dia_skip_preanalysis.config | 48 +++++++++++++++++++
 modules.json                                |  2 +-
 nextflow.config                             |  2 +
 5 files changed, 105 insertions(+), 2 deletions(-)
 create mode 100644 conf/tests/test_dda.config
 create mode 100644 conf/tests/test_dia_skip_preanalysis.config

diff --git a/.github/workflows/extended_ci.yml b/.github/workflows/extended_ci.yml
index 42a9f48..621ab2c 100644
--- a/.github/workflows/extended_ci.yml
+++ b/.github/workflows/extended_ci.yml
@@ -114,7 +114,8 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        test_profile: ["test_latest_dia", "test_dia_quantums", "test_dia_parquet"]
+        test_profile:
+          ["test_latest_dia", "test_dia_quantums", "test_dia_parquet", "test_dda", "test_dia_skip_preanalysis"]
     env:
       NXF_ANSI_LOG: false
       CAPSULE_LOG: none
diff --git a/conf/tests/test_dda.config b/conf/tests/test_dda.config
new file mode 100644
index 0000000..c0ebb24
--- /dev/null
+++ b/conf/tests/test_dda.config
@@ -0,0 +1,52 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for testing DDA analysis (requires DIA-NN >= 2.3.2)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Tests DDA mode using the BSA dataset with --diann_dda flag.
+    Uses ghcr.io/bigbio/diann:2.3.2.
+
+    Use as follows:
+        nextflow run bigbio/quantmsdiann -profile test_dda,docker [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '12.GB',
+        time: '48.h'
+    ]
+}
+
+params {
+    config_profile_name        = 'Test profile for DDA analysis'
+    config_profile_description = 'DDA test using BSA dataset with DIA-NN 2.3.2.'
+
+    outdir = './results_dda'
+
+    // Input data - BSA DDA dataset
+    input = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/lfq_ci/BSA/BSA_design.sdrf.tsv'
+    database = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/lfq_ci/BSA/18Protein_SoCe_Tr_detergents_trace.fasta'
+
+    // DDA mode
+    diann_dda = true
+
+    // Search parameters matching BSA dataset
+    min_peptide_length = 7
+    max_peptide_length = 30
+    max_precursor_charge = 3
+    allowed_missed_cleavages = 1
+    diann_normalize = false
+    publish_dir_mode = 'symlink'
+    max_mods = 2
+}
+
+process {
+    withLabel: diann {
+        container = 'ghcr.io/bigbio/diann:2.3.2'
+    }
+}
+
+singularity.enabled = false
+docker.enabled = true
diff --git a/conf/tests/test_dia_skip_preanalysis.config b/conf/tests/test_dia_skip_preanalysis.config
new file mode 100644
index 0000000..e1968b5
--- /dev/null
+++ b/conf/tests/test_dia_skip_preanalysis.config
@@ -0,0 +1,48 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for testing skip_preliminary_analysis path
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Tests the pipeline with skip_preliminary_analysis=true, using default
+    mass accuracy parameters. Validates the untested code path in dia.nf.
+
+    Use as follows:
+        nextflow run bigbio/quantmsdiann -profile test_dia_skip_preanalysis,docker [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
+
+process {
+    resourceLimits = [
+        cpus: 4,
+        memory: '12.GB',
+        time: '48.h'
+    ]
+}
+
+params {
+    config_profile_name        = 'Test profile for skip preliminary analysis'
+    config_profile_description = 'Tests skip_preliminary_analysis path with default mass accuracy params.'
+
+    outdir = './results_skip_preanalysis'
+
+    // Input data - same as test_dia
+    input = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/dia_ci/PXD026600.sdrf.tsv'
+    database = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/dia_ci/REF_EColi_K12_UPS1_combined.fasta'
+    min_pr_mz = 350
+    max_pr_mz = 950
+    min_fr_mz = 500
+    max_fr_mz = 1500
+    min_peptide_length = 15
+    max_peptide_length = 30
+    max_precursor_charge = 3
+    allowed_missed_cleavages = 1
+    diann_normalize = false
+    publish_dir_mode = 'symlink'
+    max_mods = 2
+
+    // Skip preliminary analysis - use default mass accuracy params
+    skip_preliminary_analysis = true
+    mass_acc_ms2 = 15
+    mass_acc_ms1 = 15
+    scan_window = 8
+}
diff --git a/modules.json b/modules.json
index be82844..c0e263c 100644
--- a/modules.json
+++ b/modules.json
@@ -46,4 +46,4 @@
             }
         }
     }
-}
\ No newline at end of file
+}
diff --git a/nextflow.config b/nextflow.config
index 3340937..ef0f778 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -242,6 +242,8 @@ profiles {
     test_dia_2_2_0      { includeConfig 'conf/tests/test_dia_2_2_0.config'     }
     test_latest_dia     { includeConfig 'conf/tests/test_latest_dia.config'     }
     test_full_dia       { includeConfig 'conf/tests/test_full_dia.config'       }
+    test_dda            { includeConfig 'conf/tests/test_dda.config'           }
+    test_dia_skip_preanalysis { includeConfig 'conf/tests/test_dia_skip_preanalysis.config' }
     // DIA-NN version overrides (used by merge_ci.yml matrix)
     diann_v1_8_1        { includeConfig 'conf/diann_versions/v1_8_1.config'    }
     diann_v2_1_0        { includeConfig 'conf/diann_versions/v2_1_0.config'    }

From a13d4b3cb8b5ea20268caf84a04e1dd26195a497 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:44:56 +0100
Subject: [PATCH 08/28] feat: add --light-models, --export-quant,
 --site-ms1-quant params (#7)

- diann_light_models: 10x faster in-silico library generation
- diann_export_quant: fragment-level parquet export
- diann_site_ms1_quant: MS1 apex intensities for PTM quantification
All require DIA-NN >= 2.0.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../local/diann/final_quantification/main.nf   |  6 +++++-
 .../diann/insilico_library_generation/main.nf  |  4 +++-
 nextflow.config                                |  3 +++
 nextflow_schema.json                           | 18 ++++++++++++++++++
 4 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/modules/local/diann/final_quantification/main.nf b/modules/local/diann/final_quantification/main.nf
index 8e6c76d..fc8bbd0 100644
--- a/modules/local/diann/final_quantification/main.nf
+++ b/modules/local/diann/final_quantification/main.nf
@@ -48,7 +48,7 @@ process FINAL_QUANTIFICATION {
          '--use-quant', '--matrices', '--out', '--relaxed-prot-inf', '--pg-level',
          '--qvalue', '--window', '--individual-windows',
          '--species-genes', '--report-decoys', '--xic', '--no-norm',
-         '--monitor-mod', '--var-mod', '--fixed-mod', '--dda']
+         '--monitor-mod', '--var-mod', '--fixed-mod', '--dda', '--export-quant', '--site-ms1-quant']
     // Sort by length descending so longer flags (e.g. --individual-windows) are matched before shorter prefixes (--window)
     blocked.sort { a -> -a.length() }.each { flag ->
         def flagPattern = '(?<=^|\\s)' + java.util.regex.Pattern.quote(flag) + '(?=\\s|\$)(\\s+(?!-{1,2}[a-zA-Z])\\S+)*'
@@ -70,6 +70,8 @@ process FINAL_QUANTIFICATION {
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
     diann_use_quant = params.diann_use_quant ? "--use-quant" : ""
     diann_dda_flag = params.diann_dda ? "--dda" : ""
+    diann_export_quant = params.diann_export_quant ? "--export-quant" : ""
+    diann_site_ms1_quant = params.diann_site_ms1_quant ? "--site-ms1-quant" : ""
 
     """
     # Notes: if .quant files are passed, mzml/.d files are not accessed, so the name needs to be passed but files
@@ -100,6 +102,8 @@ process FINAL_QUANTIFICATION {
             ${diann_no_peptidoforms} \\
             ${diann_use_quant} \\
             ${diann_dda_flag} \\
+            ${diann_export_quant} \\
+            ${diann_site_ms1_quant} \\
             \${mod_flags} \\
             $args
 
diff --git a/modules/local/diann/insilico_library_generation/main.nf b/modules/local/diann/insilico_library_generation/main.nf
index 321cc2f..2937af2 100644
--- a/modules/local/diann/insilico_library_generation/main.nf
+++ b/modules/local/diann/insilico_library_generation/main.nf
@@ -30,7 +30,7 @@ process INSILICO_LIBRARY_GENERATION {
          '--missed-cleavages', '--min-pep-len', '--max-pep-len',
          '--min-pr-charge', '--max-pr-charge', '--var-mods',
          '--min-pr-mz', '--max-pr-mz', '--min-fr-mz', '--max-fr-mz',
-         '--met-excision', '--monitor-mod', '--dda']
+         '--met-excision', '--monitor-mod', '--dda', '--light-models']
     // Sort by length descending so longer flags (e.g. --fasta-search) are matched before shorter prefixes (--fasta, --f)
     blocked.sort { a -> -a.length() }.each { flag ->
         def flagPattern = '(?<=^|\\s)' + java.util.regex.Pattern.quote(flag) + '(?=\\s|\$)(\\s+(?!-{1,2}[a-zA-Z])\\S+)*'
@@ -47,6 +47,7 @@ process INSILICO_LIBRARY_GENERATION {
     met_excision = params.met_excision ? "--met-excision" : ""
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
     diann_dda_flag = params.diann_dda ? "--dda" : ""
+    diann_light_models = params.diann_light_models ? "--light-models" : ""
 
     """
     diann `cat ${diann_config}` \\
@@ -67,6 +68,7 @@ process INSILICO_LIBRARY_GENERATION {
             --verbose $params.diann_debug \\
             --gen-spec-lib \\
             ${diann_no_peptidoforms} \\
+            ${diann_light_models} \\
             ${met_excision} \\
             ${diann_dda_flag} \\
             ${args}
diff --git a/nextflow.config b/nextflow.config
index ef0f778..2ad10a1 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -56,6 +56,9 @@ params {
     diann_speclib           = null
     diann_extra_args        = null
     diann_dda               = false  // Enable DDA analysis mode (requires DIA-NN >= 2.3.2)
+    diann_light_models      = false  // add '--light-models' for 10x faster library generation (DIA-NN >= 2.0)
+    diann_export_quant      = false  // add '--export-quant' for fragment-level parquet export (DIA-NN >= 2.0)
+    diann_site_ms1_quant    = false  // add '--site-ms1-quant' for MS1 apex PTM quantification (DIA-NN >= 2.0)
 
     // Optional outputs — control which intermediate files are published
     save_speclib_tsv        = false  // Save the TSV spectral library from in-silico generation
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4a65114..4d36360 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -475,6 +475,24 @@
                     "fa_icon": "fas fa-flask",
                     "default": false
                 },
+                "diann_light_models": {
+                    "type": "boolean",
+                    "description": "Enable --light-models for 10x faster in-silico library generation (DIA-NN >= 2.0).",
+                    "fa_icon": "fas fa-bolt",
+                    "default": false
+                },
+                "diann_export_quant": {
+                    "type": "boolean",
+                    "description": "Enable --export-quant for fragment-level parquet data export (DIA-NN >= 2.0).",
+                    "fa_icon": "fas fa-file-export",
+                    "default": false
+                },
+                "diann_site_ms1_quant": {
+                    "type": "boolean",
+                    "description": "Enable --site-ms1-quant to use MS1 apex intensities for PTM site quantification (DIA-NN >= 2.0).",
+                    "fa_icon": "fas fa-crosshairs",
+                    "default": false
+                },
                 "save_speclib_tsv": {
                     "type": "boolean",
                     "default": false,

From 0c56dcb0bf4589c1d7e610e5862d6830aa448b93 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:46:53 +0100
Subject: [PATCH 09/28] =?UTF-8?q?feat:=20add=20InfinDIA=20groundwork=20?=
 =?UTF-8?q?=E2=80=94=20enable=5Finfin=5Fdia=20param=20(#10)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Experimental support for InfinDIA (DIA-NN 2.3.0+). Passes --infin-dia
to library generation when enabled. Version guard enforces >= 2.3.0.
No test config — InfinDIA requires large databases.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .../local/diann/insilico_library_generation/main.nf   |  7 ++++++-
 nextflow.config                                       |  4 ++++
 nextflow_schema.json                                  | 11 +++++++++++
 workflows/dia.nf                                      |  5 +++++
 4 files changed, 26 insertions(+), 1 deletion(-)

diff --git a/modules/local/diann/insilico_library_generation/main.nf b/modules/local/diann/insilico_library_generation/main.nf
index 2937af2..7de4665 100644
--- a/modules/local/diann/insilico_library_generation/main.nf
+++ b/modules/local/diann/insilico_library_generation/main.nf
@@ -30,7 +30,8 @@ process INSILICO_LIBRARY_GENERATION {
          '--missed-cleavages', '--min-pep-len', '--max-pep-len',
          '--min-pr-charge', '--max-pr-charge', '--var-mods',
          '--min-pr-mz', '--max-pr-mz', '--min-fr-mz', '--max-fr-mz',
-         '--met-excision', '--monitor-mod', '--dda', '--light-models']
+         '--met-excision', '--monitor-mod', '--dda', '--light-models',
+         '--infin-dia', '--pre-select']
     // Sort by length descending so longer flags (e.g. --fasta-search) are matched before shorter prefixes (--fasta, --f)
     blocked.sort { a -> -a.length() }.each { flag ->
         def flagPattern = '(?<=^|\\s)' + java.util.regex.Pattern.quote(flag) + '(?=\\s|\$)(\\s+(?!-{1,2}[a-zA-Z])\\S+)*'
@@ -48,6 +49,8 @@ process INSILICO_LIBRARY_GENERATION {
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
     diann_dda_flag = params.diann_dda ? "--dda" : ""
     diann_light_models = params.diann_light_models ? "--light-models" : ""
+    infin_dia_flag = params.enable_infin_dia ? "--infin-dia" : ""
+    pre_select_flag = params.diann_pre_select ? "--pre-select $params.diann_pre_select" : ""
 
     """
     diann `cat ${diann_config}` \\
@@ -69,6 +72,8 @@ process INSILICO_LIBRARY_GENERATION {
             --gen-spec-lib \\
             ${diann_no_peptidoforms} \\
             ${diann_light_models} \\
+            ${infin_dia_flag} \\
+            ${pre_select_flag} \\
             ${met_excision} \\
             ${diann_dda_flag} \\
             ${args}
diff --git a/nextflow.config b/nextflow.config
index 2ad10a1..0f1ece2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -60,6 +60,10 @@ params {
     diann_export_quant      = false  // add '--export-quant' for fragment-level parquet export (DIA-NN >= 2.0)
     diann_site_ms1_quant    = false  // add '--site-ms1-quant' for MS1 apex PTM quantification (DIA-NN >= 2.0)
 
+    // DIA-NN: InfinDIA (experimental, v2.3.0+)
+    enable_infin_dia        = false  // Enable InfinDIA for ultra-large search spaces
+    diann_pre_select        = null   // --pre-select N precursor limit for InfinDIA
+
     // Optional outputs — control which intermediate files are published
     save_speclib_tsv        = false  // Save the TSV spectral library from in-silico generation
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 4d36360..f082614 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -493,6 +493,17 @@
                     "fa_icon": "fas fa-crosshairs",
                     "default": false
                 },
+                "enable_infin_dia": {
+                    "type": "boolean",
+                    "description": "Enable InfinDIA for ultra-large search spaces (DIA-NN >= 2.3.0). Experimental.",
+                    "fa_icon": "fas fa-infinity",
+                    "default": false
+                },
+                "diann_pre_select": {
+                    "type": "integer",
+                    "description": "Set --pre-select N precursor limit for InfinDIA pre-search.",
+                    "fa_icon": "fas fa-filter"
+                },
                 "save_speclib_tsv": {
                     "type": "boolean",
                     "default": false,
diff --git a/workflows/dia.nf b/workflows/dia.nf
index 7041d80..899d226 100644
--- a/workflows/dia.nf
+++ b/workflows/dia.nf
@@ -41,6 +41,11 @@ workflow DIA {
         error("DDA mode (--diann_dda) requires DIA-NN >= 2.3.2. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
     }
 
+    // Version guard for InfinDIA
+    if (params.enable_infin_dia && params.diann_version < '2.3.0') {
+        error("InfinDIA requires DIA-NN >= 2.3.0. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
+    }
+
     ch_searchdb = channel.fromPath(params.database, checkIfExists: true)
         .ifEmpty { error("No protein database found at '${params.database}'. Provide --database <path/to/proteins.fasta>") }
         .first()

From e69d7f2df75bb2fceeb2e31d19dba7daf438a843 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:49:50 +0100
Subject: [PATCH 10/28] docs: add comprehensive parameter reference (#1)

Complete reference for all ~70 pipeline parameters grouped by category
with types, defaults, descriptions, and version requirements.

Closes #1

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 docs/parameters.md | 162 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 162 insertions(+)
 create mode 100644 docs/parameters.md

diff --git a/docs/parameters.md b/docs/parameters.md
new file mode 100644
index 0000000..fb6f229
--- /dev/null
+++ b/docs/parameters.md
@@ -0,0 +1,162 @@
+# Pipeline Parameters
+
+Complete reference for all `bigbio/quantmsdiann` pipeline parameters.
+Parameters are specified on the command line as `--parameter_name value` or
+in a Nextflow config file.
+
+## Input/Output Options
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--input` | string | `null` | Path or URI to an SDRF file (.sdrf, .tsv, or .csv). Acquisition method, labelling type, enzyme, and fixed modifications are read exclusively from the SDRF. |
+| `--database` | string | `null` | Path to the FASTA protein database. Must not contain decoys for DIA data. |
+| `--outdir` | string | `./results` | Output directory where results will be saved. |
+| `--publish_dir_mode` | string | `copy` | Method used to save pipeline results. Options: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. |
+| `--root_folder` | string | `null` | Root folder in which spectrum files specified in the SDRF are searched. Used when files are available locally. |
+| `--local_input_type` | string | `mzML` | Override the file type/extension of filenames in the SDRF when using `--root_folder`. Options: `mzML`, `raw`, `d`, `dia`. Compressed variants (.gz, .tar, .tar.gz, .zip) are supported. |
+
+## SDRF Validation
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--use_ols_cache_only` | boolean | `true` | Use only the cached Ontology Lookup Service (OLS) for term validation, avoiding network requests. |
+
+## File Preparation
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--reindex_mzml` | boolean | `true` | Force re-indexing of input mzML files at the start of the pipeline. Also fixes common issues in slightly incomplete mzMLs. |
+| `--mzml_statistics` | boolean | `false` | Compute MS1/MS2 statistics from mzML files. Generates `*_ms_info.parquet` for QC reporting. Bruker .d files are always skipped. |
+| `--mzml_features` | boolean | `false` | Compute MS1-level features during the mzML statistics step. Only available for mzML files. |
+| `--convert_dotd` | boolean | `false` | Convert Bruker .d files to mzML format before processing. |
+
+## Search Parameters
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--met_excision` | boolean | `true` | Account for N-terminal methionine excision during database search. |
+| `--allowed_missed_cleavages` | integer | `2` | Maximum number of allowed missed enzyme cleavages per peptide. |
+| `--precursor_mass_tolerance` | integer | `5` | Precursor mass tolerance for database search. See also `--precursor_mass_tolerance_unit`. Can be overridden from SDRF. |
+| `--precursor_mass_tolerance_unit` | string | `ppm` | Unit for precursor mass tolerance. Options: `ppm`, `Da`. |
+| `--fragment_mass_tolerance` | number | `0.03` | Fragment mass tolerance for database search. Can be overridden from SDRF. |
+| `--fragment_mass_tolerance_unit` | string | `Da` | Unit for fragment mass tolerance. Options: `ppm`, `Da`. |
+| `--variable_mods` | string | `Oxidation (M)` | Comma-separated list of variable modifications using Unimod names (e.g. `Oxidation (M),Carbamidomethyl (C)`). Can be overridden from SDRF. |
+| `--min_precursor_charge` | integer | `2` | Minimum precursor ion charge. |
+| `--max_precursor_charge` | integer | `4` | Maximum precursor ion charge. |
+| `--min_peptide_length` | integer | `6` | Minimum peptide length to consider. |
+| `--max_peptide_length` | integer | `40` | Maximum peptide length to consider. |
+| `--max_mods` | integer | `3` | Maximum number of modifications per peptide. Large values may slow the search considerably. |
+| `--min_pr_mz` | number | `400` | Minimum precursor m/z for in-silico library generation or library-free search. |
+| `--max_pr_mz` | number | `2400` | Maximum precursor m/z for in-silico library generation or library-free search. |
+| `--min_fr_mz` | number | `100` | Minimum fragment m/z for in-silico library generation or library-free search. |
+| `--max_fr_mz` | number | `1800` | Maximum fragment m/z for in-silico library generation or library-free search. |
+
+## DIA-NN General
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--diann_version` | string | `1.8.1` | DIA-NN version used by the workflow. Controls version-dependent flags (e.g. `--monitor-mod` for 1.8.x). |
+| `--diann_debug` | integer | `3` | DIA-NN debug/verbosity level. Allowed values: 0, 1, 2, 3, 4. |
+| `--diann_speclib` | string | `null` | Path to an existing spectral library. If provided, the pipeline uses it instead of predicting one from the FASTA. |
+| `--diann_extra_args` | string | `null` | Extra command-line arguments appended to all DIA-NN steps. Flags incompatible with a specific step are automatically stripped with a warning. |
+| `--diann_dda` | boolean | `false` | Enable DDA (Data-Dependent Acquisition) analysis mode. Passes `--dda` to all DIA-NN steps. Requires DIA-NN >= 2.3.2. Beta feature. |
+| `--diann_light_models` | boolean | `false` | Enable `--light-models` for 10x faster in-silico library generation. Requires DIA-NN >= 2.0. |
+| `--diann_export_quant` | boolean | `false` | Enable `--export-quant` for fragment-level parquet data export. Requires DIA-NN >= 2.0. |
+| `--diann_site_ms1_quant` | boolean | `false` | Enable `--site-ms1-quant` to use MS1 apex intensities for PTM site quantification. Requires DIA-NN >= 2.0. |
+
+## Mass Accuracy and Calibration
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--mass_acc_automatic` | boolean | `true` | Automatically determine the MS2 mass accuracy setting. |
+| `--mass_acc_ms1` | number | `15` | MS1 mass accuracy in ppm. Overrides automatic calibration when set. Maps to DIA-NN `--mass-acc-ms1`. |
+| `--mass_acc_ms2` | number | `15` | MS2 mass accuracy in ppm. Overrides automatic calibration when set. Maps to DIA-NN `--mass-acc`. |
+| `--scan_window` | integer | `8` | Scan window radius. Ideally approximately equal to the average number of data points per peak. |
+| `--scan_window_automatic` | boolean | `true` | Automatically determine the scan window setting. |
+| `--quick_mass_acc` | boolean | `true` | Use a fast heuristic algorithm instead of ID-number optimization when choosing MS2 mass accuracy automatically. |
+| `--performance_mode` | boolean | `true` | Enable low-RAM/high-speed mode. Adds `--min-corr 2 --corr-diff 1 --time-corr-only` to DIA-NN. |
+
+## Bruker/timsTOF
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--diann_tims_sum` | boolean | `false` | Enable `--quant-tims-sum` for slice/scanning timsTOF methods. Highly recommended for Synchro-PASEF. |
+| `--diann_im_window` | number | `null` | Set `--im-window` to ensure the ion mobility extraction window is not smaller than the specified value. |
+
+## PTM Localization
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--enable_mod_localization` | boolean | `false` | Enable modification localization scoring in DIA-NN (`--monitor-mod`). |
+| `--mod_localization` | string | `Phospho (S),Phospho (T),Phospho (Y)` | Comma-separated modification names or UniMod accessions for localization (e.g. `UniMod:21,UniMod:1`). |
+
+## Library Generation
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--save_speclib_tsv` | boolean | `false` | Publish the human-readable TSV spectral library from the in-silico generation step to the output directory. |
+
+## Preliminary Analysis
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--skip_preliminary_analysis` | boolean | `false` | Skip the preliminary analysis step and use the provided spectral library as-is instead of building a local consensus library. |
+| `--empirical_assembly_log` | string | `null` | Path to a pre-existing empirical assembly log file. Only used when `--skip_preliminary_analysis true` and `--diann_speclib` are set. |
+| `--random_preanalysis` | boolean | `false` | Enable random selection of spectrum files for empirical library generation. |
+| `--random_preanalysis_seed` | integer | `42` | Random seed for spectrum file selection when `--random_preanalysis` is enabled. |
+| `--empirical_assembly_ms_n` | integer | `200` | Number of randomly selected spectrum files used for empirical library assembly. |
+
+## Quantification and Output
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--pg_level` | integer | `2` | Protein inference mode. 0 = isoforms, 1 = protein names from FASTA, 2 = genes. |
+| `--species_genes` | boolean | `false` | Add the organism identifier to gene names in DIA-NN output. |
+| `--diann_normalize` | boolean | `true` | Enable cross-run normalization in DIA-NN. |
+| `--diann_report_decoys` | boolean | `false` | Include decoy PSMs in the main .parquet report. |
+| `--diann_export_xic` | boolean | `false` | Extract MS1/fragment chromatograms for identified precursors (10 s window from elution apex). |
+| `--diann_no_peptidoforms` | boolean | `false` | Disable automatic peptidoform scoring when variable modifications are declared. Not recommended by DIA-NN authors. |
+| `--diann_use_quant` | boolean | `true` | Reuse existing .quant files if available during final quantification (`--use-quant`). |
+| `--quantums` | boolean | `false` | Enable QuantUMS quantification (DIA-NN `--direct-quant`). |
+| `--quantums_train_runs` | string | `null` | Run index range for QuantUMS training (e.g. `0:5`). Maps to `--quant-train-runs`. |
+| `--quantums_sel_runs` | integer | `null` | Number of automatically selected runs for QuantUMS training. Must be >= 6. Maps to `--quant-sel-runs`. |
+| `--quantums_params` | string | `null` | Pre-calculated QuantUMS parameters. Maps to `--quant-params`. |
+
+## DDA Mode
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--diann_dda` | boolean | `false` | Enable DDA analysis mode. Passes `--dda` to all DIA-NN steps. Requires DIA-NN >= 2.3.2 (use `-profile diann_v2_3_2`). This is a beta feature with known limitations; see the usage documentation for details. |
+
+> **Note:** DDA support requires DIA-NN >= 2.3.2. Enable this profile with
+> `-profile diann_v2_3_2`. The DDA mode is experimental and may not support
+> all pipeline features available in DIA mode.
+
+## InfinDIA (Experimental)
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--enable_infin_dia` | boolean | `false` | Enable InfinDIA for ultra-large search spaces. Requires DIA-NN >= 2.3.0. Experimental. |
+| `--diann_pre_select` | integer | `null` | Precursor limit (`--pre-select N`) for InfinDIA pre-search. |
+
+> **Note:** InfinDIA requires DIA-NN >= 2.3.0 and is considered experimental.
+
+## Quality Control
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--enable_pmultiqc` | boolean | `true` | Generate a pmultiqc proteomics QC report. |
+| `--pmultiqc_idxml_skip` | boolean | `true` | Skip idXML files (do not generate search engine score plots) in the pmultiqc report. |
+| `--contaminant_string` | string | `CONT` | Contaminant affix string used by pmultiqc to identify contaminant proteins. |
+| `--protein_level_fdr_cutoff` | number | `0.01` | Experiment-wide protein/protein-group-level FDR cutoff. |
+
+## MultiQC
+
+| Parameter | Type | Default | Description |
+|---|---|---|---|
+| `--multiqc_config` | string | `null` | Path to a custom MultiQC configuration file. |
+| `--multiqc_title` | string | `null` | Custom title for the MultiQC report. Used as page header and default filename. |
+| `--multiqc_logo` | string | `null` | Path to a custom logo file for the MultiQC report. Must also be set in the MultiQC config. |
+| `--skip_table_plots` | boolean | `false` | Skip protein/peptide table plots in pmultiqc. Useful for very large datasets. |
+| `--max_multiqc_email_size` | string | `25.MB` | Maximum file size for MultiQC report attachments in summary emails. |
+| `--multiqc_methods_description` | string | `null` | Path to a custom YAML file containing an HTML methods description for MultiQC. |

From 52fa59f239434f604a3de3213073f0ef4bc054f7 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 16:52:03 +0100
Subject: [PATCH 11/28] docs: complete usage.md, output.md, citations, README
 (#1, #3, #9, #15)

- DDA mode documentation with limitations
- Missing param sections (preprocessing, extra_args scope, verbose output)
- DIA-NN version selection guide
- Parquet vs TSV output explanation
- MSstats format section
- pmultiqc citation added
- README updated with version table and parameter reference link

Closes #3, #9, #15

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 CITATIONS.md   |  4 ++++
 README.md      | 11 +++++++++
 docs/output.md |  8 +++++++
 docs/usage.md  | 60 ++++++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 83 insertions(+)

diff --git a/CITATIONS.md b/CITATIONS.md
index be290a2..84be394 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -34,6 +34,10 @@
 
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
+- [pmultiqc](https://github.com/bigbio/pmultiqc/)
+
+  > Perez-Riverol Y, et al. (2024). pmultiqc: A comprehensive tool for quality control of proteomics data. Nature Methods.
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)
diff --git a/README.md b/README.md
index 02d6f3c..e69211a 100644
--- a/README.md
+++ b/README.md
@@ -34,6 +34,17 @@ The pipeline takes [SDRF](https://github.com/bigbio/proteomics-metadata-standard
 8. **MSstats conversion** — DIA-NN report to MSstats-compatible format
 9. **Quality control** — interactive QC report via [pmultiqc](https://github.com/bigbio/pmultiqc)
 
+### Supported DIA-NN Versions
+
+| Version | Profile        | Key Features          |
+| ------- | -------------- | --------------------- |
+| 1.8.1   | (default)      | Core DIA analysis     |
+| 2.1.0   | `diann_v2_1_0` | Native .raw support   |
+| 2.2.0   | `diann_v2_2_0` | Speed optimizations   |
+| 2.3.2   | `diann_v2_3_2` | DDA support, InfinDIA |
+
+See [docs/parameters.md](docs/parameters.md) for the full parameter reference.
+
 ## Quick start
 
 > [!NOTE]
diff --git a/docs/output.md b/docs/output.md
index 9af5b47..2cb6c5c 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -70,6 +70,14 @@ results/
   - `quant_tables/diann_report.unique_genes_matrix.tsv` - Unique gene quantification matrix
   - `quant_tables/out_msstats_in.csv` - MSstats-compatible quantification table
 
+### Parquet vs TSV Output (DIA-NN 2.0+)
+
+DIA-NN 2.0+ outputs the main report in Parquet format instead of TSV. The pipeline handles both formats automatically via the `diann_report.{tsv,parquet}` output pattern. Downstream tools (quantms-utils, pmultiqc) support both formats.
+
+### MSstats-Compatible Output
+
+The pipeline generates `out_msstats_in.csv` — a CSV file in MSstats-compatible format suitable for downstream statistical analysis with MSstats or similar tools. This is a format conversion (via `quantmsutilsc diann2msstats`), not an MSstats analysis.
+
 ### Optional Output Files
 
 These files are not published by default. Enable them with `save_*` parameters or `ext.*` config properties (see [Usage: Optional outputs](usage.md#optional-outputs)).
diff --git a/docs/usage.md b/docs/usage.md
index 181bfd3..ae7c68c 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -54,6 +54,66 @@ For Synchro-PASEF data, enable `--diann_tims_sum` (which adds `--quant-tims-sum`
 > [!NOTE]
 > The pipeline will emit a warning during PRELIMINARY_ANALYSIS if it detects `.d` files with automatic mass accuracy calibration enabled, recommending to set tolerances via SDRF or pipeline parameters.
 
+### DDA Analysis Mode (Beta)
+
+DIA-NN 2.3.2+ supports DDA data analysis via the `--dda` flag. Enable it with:
+
+```bash
+nextflow run bigbio/quantmsdiann \
+  --input sdrf.tsv \
+  --database proteins.fasta \
+  --diann_dda true \
+  -profile diann_v2_3_2,docker
+```
+
+**Limitations (beta feature):**
+
+- Only trust: q-values, PEP values, RT/IM values, Ms1.Apex.Area, Normalisation.Factor
+- PTM localization probabilities are **unreliable** with DDA data
+- MBR requires MS2-level evidence (DIA-like, not classical DDA MBR)
+- No isobaric labeling or reporter-tag quantification
+- Primary use cases: legacy DDA reanalysis, spectral library creation, immunopeptidomics
+
+The pipeline uses the same workflow for DDA as DIA — the `--dda` flag is passed to all DIA-NN steps automatically.
+
+### Preprocessing Options
+
+- `--reindex_mzml` (default: true) — Re-index mzML files before processing. Disable with `--reindex_mzml false` if files are already indexed.
+- `--mzml_statistics` (default: false) — Generate mzML statistics (parquet format) for QC.
+- `--mzml_features` (default: false) — Enable feature detection in mzML statistics.
+- `--convert_dotd` (default: false) — Convert Bruker .d files to mzML via tdf2mzml instead of passing natively to DIA-NN.
+
+### Passing Extra Arguments to DIA-NN
+
+Use `--diann_extra_args` to pass additional flags to all DIA-NN steps. The pipeline validates and strips flags it manages internally to prevent conflicts.
+
+Managed flags (stripped with a warning if passed via extra_args): `--lib`, `--f`, `--fasta`, `--threads`, `--verbose`, `--temp`, `--out`, `--matrices`, `--use-quant`, `--gen-spec-lib`, `--mass-acc`, `--mass-acc-ms1`, `--window`, `--var-mod`, `--fixed-mod`, `--monitor-mod`, and others.
+
+To enable this, add `includeConfig 'conf/modules/dia.config'` to your configuration (already included by default).
+
+### DIA-NN Version Selection
+
+The default DIA-NN version is 1.8.1. To use a different version:
+
+| Version | Profile                 | Features                            |
+| ------- | ----------------------- | ----------------------------------- |
+| 1.8.1   | (default)               | Core DIA analysis                   |
+| 2.1.0   | `-profile diann_v2_1_0` | Native .raw support, reduced memory |
+| 2.2.0   | `-profile diann_v2_2_0` | Speed optimizations                 |
+| 2.3.2   | `-profile diann_v2_3_2` | DDA support, InfinDIA               |
+
+Example: `nextflow run bigbio/quantmsdiann -profile test_dia,docker,diann_v2_2_0`
+
+### Verbose Module Output
+
+Use `-profile verbose_modules` to publish intermediate files from all pipeline steps:
+
+```bash
+nextflow run bigbio/quantmsdiann -profile test_dia,docker,verbose_modules --outdir results
+```
+
+This publishes ThermoRawFileParser conversions, mzML indexing results, per-file DIA-NN logs, and spectral library intermediates.
+
 ### Pipeline settings via params file
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`:

From 21fc10caea81099e910216c315a6ea662487e563 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 18:36:35 +0100
Subject: [PATCH 12/28] style: apply prettier formatting to parameters.md

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 docs/parameters.md | 202 ++++++++++++++++++++++-----------------------
 1 file changed, 101 insertions(+), 101 deletions(-)

diff --git a/docs/parameters.md b/docs/parameters.md
index fb6f229..aa0b645 100644
--- a/docs/parameters.md
+++ b/docs/parameters.md
@@ -6,126 +6,126 @@ in a Nextflow config file.
 
 ## Input/Output Options
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--input` | string | `null` | Path or URI to an SDRF file (.sdrf, .tsv, or .csv). Acquisition method, labelling type, enzyme, and fixed modifications are read exclusively from the SDRF. |
-| `--database` | string | `null` | Path to the FASTA protein database. Must not contain decoys for DIA data. |
-| `--outdir` | string | `./results` | Output directory where results will be saved. |
-| `--publish_dir_mode` | string | `copy` | Method used to save pipeline results. Options: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`. |
-| `--root_folder` | string | `null` | Root folder in which spectrum files specified in the SDRF are searched. Used when files are available locally. |
-| `--local_input_type` | string | `mzML` | Override the file type/extension of filenames in the SDRF when using `--root_folder`. Options: `mzML`, `raw`, `d`, `dia`. Compressed variants (.gz, .tar, .tar.gz, .zip) are supported. |
+| Parameter            | Type   | Default     | Description                                                                                                                                                                             |
+| -------------------- | ------ | ----------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `--input`            | string | `null`      | Path or URI to an SDRF file (.sdrf, .tsv, or .csv). Acquisition method, labelling type, enzyme, and fixed modifications are read exclusively from the SDRF.                             |
+| `--database`         | string | `null`      | Path to the FASTA protein database. Must not contain decoys for DIA data.                                                                                                               |
+| `--outdir`           | string | `./results` | Output directory where results will be saved.                                                                                                                                           |
+| `--publish_dir_mode` | string | `copy`      | Method used to save pipeline results. Options: `symlink`, `rellink`, `link`, `copy`, `copyNoFollow`, `move`.                                                                            |
+| `--root_folder`      | string | `null`      | Root folder in which spectrum files specified in the SDRF are searched. Used when files are available locally.                                                                          |
+| `--local_input_type` | string | `mzML`      | Override the file type/extension of filenames in the SDRF when using `--root_folder`. Options: `mzML`, `raw`, `d`, `dia`. Compressed variants (.gz, .tar, .tar.gz, .zip) are supported. |
 
 ## SDRF Validation
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--use_ols_cache_only` | boolean | `true` | Use only the cached Ontology Lookup Service (OLS) for term validation, avoiding network requests. |
+| Parameter              | Type    | Default | Description                                                                                       |
+| ---------------------- | ------- | ------- | ------------------------------------------------------------------------------------------------- |
+| `--use_ols_cache_only` | boolean | `true`  | Use only the cached Ontology Lookup Service (OLS) for term validation, avoiding network requests. |
 
 ## File Preparation
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--reindex_mzml` | boolean | `true` | Force re-indexing of input mzML files at the start of the pipeline. Also fixes common issues in slightly incomplete mzMLs. |
+| Parameter           | Type    | Default | Description                                                                                                                     |
+| ------------------- | ------- | ------- | ------------------------------------------------------------------------------------------------------------------------------- |
+| `--reindex_mzml`    | boolean | `true`  | Force re-indexing of input mzML files at the start of the pipeline. Also fixes common issues in slightly incomplete mzMLs.      |
 | `--mzml_statistics` | boolean | `false` | Compute MS1/MS2 statistics from mzML files. Generates `*_ms_info.parquet` for QC reporting. Bruker .d files are always skipped. |
-| `--mzml_features` | boolean | `false` | Compute MS1-level features during the mzML statistics step. Only available for mzML files. |
-| `--convert_dotd` | boolean | `false` | Convert Bruker .d files to mzML format before processing. |
+| `--mzml_features`   | boolean | `false` | Compute MS1-level features during the mzML statistics step. Only available for mzML files.                                      |
+| `--convert_dotd`    | boolean | `false` | Convert Bruker .d files to mzML format before processing.                                                                       |
 
 ## Search Parameters
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--met_excision` | boolean | `true` | Account for N-terminal methionine excision during database search. |
-| `--allowed_missed_cleavages` | integer | `2` | Maximum number of allowed missed enzyme cleavages per peptide. |
-| `--precursor_mass_tolerance` | integer | `5` | Precursor mass tolerance for database search. See also `--precursor_mass_tolerance_unit`. Can be overridden from SDRF. |
-| `--precursor_mass_tolerance_unit` | string | `ppm` | Unit for precursor mass tolerance. Options: `ppm`, `Da`. |
-| `--fragment_mass_tolerance` | number | `0.03` | Fragment mass tolerance for database search. Can be overridden from SDRF. |
-| `--fragment_mass_tolerance_unit` | string | `Da` | Unit for fragment mass tolerance. Options: `ppm`, `Da`. |
-| `--variable_mods` | string | `Oxidation (M)` | Comma-separated list of variable modifications using Unimod names (e.g. `Oxidation (M),Carbamidomethyl (C)`). Can be overridden from SDRF. |
-| `--min_precursor_charge` | integer | `2` | Minimum precursor ion charge. |
-| `--max_precursor_charge` | integer | `4` | Maximum precursor ion charge. |
-| `--min_peptide_length` | integer | `6` | Minimum peptide length to consider. |
-| `--max_peptide_length` | integer | `40` | Maximum peptide length to consider. |
-| `--max_mods` | integer | `3` | Maximum number of modifications per peptide. Large values may slow the search considerably. |
-| `--min_pr_mz` | number | `400` | Minimum precursor m/z for in-silico library generation or library-free search. |
-| `--max_pr_mz` | number | `2400` | Maximum precursor m/z for in-silico library generation or library-free search. |
-| `--min_fr_mz` | number | `100` | Minimum fragment m/z for in-silico library generation or library-free search. |
-| `--max_fr_mz` | number | `1800` | Maximum fragment m/z for in-silico library generation or library-free search. |
+| Parameter                         | Type    | Default         | Description                                                                                                                                |
+| --------------------------------- | ------- | --------------- | ------------------------------------------------------------------------------------------------------------------------------------------ |
+| `--met_excision`                  | boolean | `true`          | Account for N-terminal methionine excision during database search.                                                                         |
+| `--allowed_missed_cleavages`      | integer | `2`             | Maximum number of allowed missed enzyme cleavages per peptide.                                                                             |
+| `--precursor_mass_tolerance`      | integer | `5`             | Precursor mass tolerance for database search. See also `--precursor_mass_tolerance_unit`. Can be overridden from SDRF.                     |
+| `--precursor_mass_tolerance_unit` | string  | `ppm`           | Unit for precursor mass tolerance. Options: `ppm`, `Da`.                                                                                   |
+| `--fragment_mass_tolerance`       | number  | `0.03`          | Fragment mass tolerance for database search. Can be overridden from SDRF.                                                                  |
+| `--fragment_mass_tolerance_unit`  | string  | `Da`            | Unit for fragment mass tolerance. Options: `ppm`, `Da`.                                                                                    |
+| `--variable_mods`                 | string  | `Oxidation (M)` | Comma-separated list of variable modifications using Unimod names (e.g. `Oxidation (M),Carbamidomethyl (C)`). Can be overridden from SDRF. |
+| `--min_precursor_charge`          | integer | `2`             | Minimum precursor ion charge.                                                                                                              |
+| `--max_precursor_charge`          | integer | `4`             | Maximum precursor ion charge.                                                                                                              |
+| `--min_peptide_length`            | integer | `6`             | Minimum peptide length to consider.                                                                                                        |
+| `--max_peptide_length`            | integer | `40`            | Maximum peptide length to consider.                                                                                                        |
+| `--max_mods`                      | integer | `3`             | Maximum number of modifications per peptide. Large values may slow the search considerably.                                                |
+| `--min_pr_mz`                     | number  | `400`           | Minimum precursor m/z for in-silico library generation or library-free search.                                                             |
+| `--max_pr_mz`                     | number  | `2400`          | Maximum precursor m/z for in-silico library generation or library-free search.                                                             |
+| `--min_fr_mz`                     | number  | `100`           | Minimum fragment m/z for in-silico library generation or library-free search.                                                              |
+| `--max_fr_mz`                     | number  | `1800`          | Maximum fragment m/z for in-silico library generation or library-free search.                                                              |
 
 ## DIA-NN General
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--diann_version` | string | `1.8.1` | DIA-NN version used by the workflow. Controls version-dependent flags (e.g. `--monitor-mod` for 1.8.x). |
-| `--diann_debug` | integer | `3` | DIA-NN debug/verbosity level. Allowed values: 0, 1, 2, 3, 4. |
-| `--diann_speclib` | string | `null` | Path to an existing spectral library. If provided, the pipeline uses it instead of predicting one from the FASTA. |
-| `--diann_extra_args` | string | `null` | Extra command-line arguments appended to all DIA-NN steps. Flags incompatible with a specific step are automatically stripped with a warning. |
-| `--diann_dda` | boolean | `false` | Enable DDA (Data-Dependent Acquisition) analysis mode. Passes `--dda` to all DIA-NN steps. Requires DIA-NN >= 2.3.2. Beta feature. |
-| `--diann_light_models` | boolean | `false` | Enable `--light-models` for 10x faster in-silico library generation. Requires DIA-NN >= 2.0. |
-| `--diann_export_quant` | boolean | `false` | Enable `--export-quant` for fragment-level parquet data export. Requires DIA-NN >= 2.0. |
-| `--diann_site_ms1_quant` | boolean | `false` | Enable `--site-ms1-quant` to use MS1 apex intensities for PTM site quantification. Requires DIA-NN >= 2.0. |
+| Parameter                | Type    | Default | Description                                                                                                                                   |
+| ------------------------ | ------- | ------- | --------------------------------------------------------------------------------------------------------------------------------------------- |
+| `--diann_version`        | string  | `1.8.1` | DIA-NN version used by the workflow. Controls version-dependent flags (e.g. `--monitor-mod` for 1.8.x).                                       |
+| `--diann_debug`          | integer | `3`     | DIA-NN debug/verbosity level. Allowed values: 0, 1, 2, 3, 4.                                                                                  |
+| `--diann_speclib`        | string  | `null`  | Path to an existing spectral library. If provided, the pipeline uses it instead of predicting one from the FASTA.                             |
+| `--diann_extra_args`     | string  | `null`  | Extra command-line arguments appended to all DIA-NN steps. Flags incompatible with a specific step are automatically stripped with a warning. |
+| `--diann_dda`            | boolean | `false` | Enable DDA (Data-Dependent Acquisition) analysis mode. Passes `--dda` to all DIA-NN steps. Requires DIA-NN >= 2.3.2. Beta feature.            |
+| `--diann_light_models`   | boolean | `false` | Enable `--light-models` for 10x faster in-silico library generation. Requires DIA-NN >= 2.0.                                                  |
+| `--diann_export_quant`   | boolean | `false` | Enable `--export-quant` for fragment-level parquet data export. Requires DIA-NN >= 2.0.                                                       |
+| `--diann_site_ms1_quant` | boolean | `false` | Enable `--site-ms1-quant` to use MS1 apex intensities for PTM site quantification. Requires DIA-NN >= 2.0.                                    |
 
 ## Mass Accuracy and Calibration
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--mass_acc_automatic` | boolean | `true` | Automatically determine the MS2 mass accuracy setting. |
-| `--mass_acc_ms1` | number | `15` | MS1 mass accuracy in ppm. Overrides automatic calibration when set. Maps to DIA-NN `--mass-acc-ms1`. |
-| `--mass_acc_ms2` | number | `15` | MS2 mass accuracy in ppm. Overrides automatic calibration when set. Maps to DIA-NN `--mass-acc`. |
-| `--scan_window` | integer | `8` | Scan window radius. Ideally approximately equal to the average number of data points per peak. |
-| `--scan_window_automatic` | boolean | `true` | Automatically determine the scan window setting. |
-| `--quick_mass_acc` | boolean | `true` | Use a fast heuristic algorithm instead of ID-number optimization when choosing MS2 mass accuracy automatically. |
-| `--performance_mode` | boolean | `true` | Enable low-RAM/high-speed mode. Adds `--min-corr 2 --corr-diff 1 --time-corr-only` to DIA-NN. |
+| Parameter                 | Type    | Default | Description                                                                                                     |
+| ------------------------- | ------- | ------- | --------------------------------------------------------------------------------------------------------------- |
+| `--mass_acc_automatic`    | boolean | `true`  | Automatically determine the MS2 mass accuracy setting.                                                          |
+| `--mass_acc_ms1`          | number  | `15`    | MS1 mass accuracy in ppm. Overrides automatic calibration when set. Maps to DIA-NN `--mass-acc-ms1`.            |
+| `--mass_acc_ms2`          | number  | `15`    | MS2 mass accuracy in ppm. Overrides automatic calibration when set. Maps to DIA-NN `--mass-acc`.                |
+| `--scan_window`           | integer | `8`     | Scan window radius. Ideally approximately equal to the average number of data points per peak.                  |
+| `--scan_window_automatic` | boolean | `true`  | Automatically determine the scan window setting.                                                                |
+| `--quick_mass_acc`        | boolean | `true`  | Use a fast heuristic algorithm instead of ID-number optimization when choosing MS2 mass accuracy automatically. |
+| `--performance_mode`      | boolean | `true`  | Enable low-RAM/high-speed mode. Adds `--min-corr 2 --corr-diff 1 --time-corr-only` to DIA-NN.                   |
 
 ## Bruker/timsTOF
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--diann_tims_sum` | boolean | `false` | Enable `--quant-tims-sum` for slice/scanning timsTOF methods. Highly recommended for Synchro-PASEF. |
-| `--diann_im_window` | number | `null` | Set `--im-window` to ensure the ion mobility extraction window is not smaller than the specified value. |
+| Parameter           | Type    | Default | Description                                                                                             |
+| ------------------- | ------- | ------- | ------------------------------------------------------------------------------------------------------- |
+| `--diann_tims_sum`  | boolean | `false` | Enable `--quant-tims-sum` for slice/scanning timsTOF methods. Highly recommended for Synchro-PASEF.     |
+| `--diann_im_window` | number  | `null`  | Set `--im-window` to ensure the ion mobility extraction window is not smaller than the specified value. |
 
 ## PTM Localization
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--enable_mod_localization` | boolean | `false` | Enable modification localization scoring in DIA-NN (`--monitor-mod`). |
-| `--mod_localization` | string | `Phospho (S),Phospho (T),Phospho (Y)` | Comma-separated modification names or UniMod accessions for localization (e.g. `UniMod:21,UniMod:1`). |
+| Parameter                   | Type    | Default                               | Description                                                                                           |
+| --------------------------- | ------- | ------------------------------------- | ----------------------------------------------------------------------------------------------------- |
+| `--enable_mod_localization` | boolean | `false`                               | Enable modification localization scoring in DIA-NN (`--monitor-mod`).                                 |
+| `--mod_localization`        | string  | `Phospho (S),Phospho (T),Phospho (Y)` | Comma-separated modification names or UniMod accessions for localization (e.g. `UniMod:21,UniMod:1`). |
 
 ## Library Generation
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
+| Parameter            | Type    | Default | Description                                                                                                 |
+| -------------------- | ------- | ------- | ----------------------------------------------------------------------------------------------------------- |
 | `--save_speclib_tsv` | boolean | `false` | Publish the human-readable TSV spectral library from the in-silico generation step to the output directory. |
 
 ## Preliminary Analysis
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--skip_preliminary_analysis` | boolean | `false` | Skip the preliminary analysis step and use the provided spectral library as-is instead of building a local consensus library. |
-| `--empirical_assembly_log` | string | `null` | Path to a pre-existing empirical assembly log file. Only used when `--skip_preliminary_analysis true` and `--diann_speclib` are set. |
-| `--random_preanalysis` | boolean | `false` | Enable random selection of spectrum files for empirical library generation. |
-| `--random_preanalysis_seed` | integer | `42` | Random seed for spectrum file selection when `--random_preanalysis` is enabled. |
-| `--empirical_assembly_ms_n` | integer | `200` | Number of randomly selected spectrum files used for empirical library assembly. |
+| Parameter                     | Type    | Default | Description                                                                                                                          |
+| ----------------------------- | ------- | ------- | ------------------------------------------------------------------------------------------------------------------------------------ |
+| `--skip_preliminary_analysis` | boolean | `false` | Skip the preliminary analysis step and use the provided spectral library as-is instead of building a local consensus library.        |
+| `--empirical_assembly_log`    | string  | `null`  | Path to a pre-existing empirical assembly log file. Only used when `--skip_preliminary_analysis true` and `--diann_speclib` are set. |
+| `--random_preanalysis`        | boolean | `false` | Enable random selection of spectrum files for empirical library generation.                                                          |
+| `--random_preanalysis_seed`   | integer | `42`    | Random seed for spectrum file selection when `--random_preanalysis` is enabled.                                                      |
+| `--empirical_assembly_ms_n`   | integer | `200`   | Number of randomly selected spectrum files used for empirical library assembly.                                                      |
 
 ## Quantification and Output
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--pg_level` | integer | `2` | Protein inference mode. 0 = isoforms, 1 = protein names from FASTA, 2 = genes. |
-| `--species_genes` | boolean | `false` | Add the organism identifier to gene names in DIA-NN output. |
-| `--diann_normalize` | boolean | `true` | Enable cross-run normalization in DIA-NN. |
-| `--diann_report_decoys` | boolean | `false` | Include decoy PSMs in the main .parquet report. |
-| `--diann_export_xic` | boolean | `false` | Extract MS1/fragment chromatograms for identified precursors (10 s window from elution apex). |
+| Parameter                 | Type    | Default | Description                                                                                                        |
+| ------------------------- | ------- | ------- | ------------------------------------------------------------------------------------------------------------------ |
+| `--pg_level`              | integer | `2`     | Protein inference mode. 0 = isoforms, 1 = protein names from FASTA, 2 = genes.                                     |
+| `--species_genes`         | boolean | `false` | Add the organism identifier to gene names in DIA-NN output.                                                        |
+| `--diann_normalize`       | boolean | `true`  | Enable cross-run normalization in DIA-NN.                                                                          |
+| `--diann_report_decoys`   | boolean | `false` | Include decoy PSMs in the main .parquet report.                                                                    |
+| `--diann_export_xic`      | boolean | `false` | Extract MS1/fragment chromatograms for identified precursors (10 s window from elution apex).                      |
 | `--diann_no_peptidoforms` | boolean | `false` | Disable automatic peptidoform scoring when variable modifications are declared. Not recommended by DIA-NN authors. |
-| `--diann_use_quant` | boolean | `true` | Reuse existing .quant files if available during final quantification (`--use-quant`). |
-| `--quantums` | boolean | `false` | Enable QuantUMS quantification (DIA-NN `--direct-quant`). |
-| `--quantums_train_runs` | string | `null` | Run index range for QuantUMS training (e.g. `0:5`). Maps to `--quant-train-runs`. |
-| `--quantums_sel_runs` | integer | `null` | Number of automatically selected runs for QuantUMS training. Must be >= 6. Maps to `--quant-sel-runs`. |
-| `--quantums_params` | string | `null` | Pre-calculated QuantUMS parameters. Maps to `--quant-params`. |
+| `--diann_use_quant`       | boolean | `true`  | Reuse existing .quant files if available during final quantification (`--use-quant`).                              |
+| `--quantums`              | boolean | `false` | Enable QuantUMS quantification (DIA-NN `--direct-quant`).                                                          |
+| `--quantums_train_runs`   | string  | `null`  | Run index range for QuantUMS training (e.g. `0:5`). Maps to `--quant-train-runs`.                                  |
+| `--quantums_sel_runs`     | integer | `null`  | Number of automatically selected runs for QuantUMS training. Must be >= 6. Maps to `--quant-sel-runs`.             |
+| `--quantums_params`       | string  | `null`  | Pre-calculated QuantUMS parameters. Maps to `--quant-params`.                                                      |
 
 ## DDA Mode
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
+| Parameter     | Type    | Default | Description                                                                                                                                                                                                   |
+| ------------- | ------- | ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `--diann_dda` | boolean | `false` | Enable DDA analysis mode. Passes `--dda` to all DIA-NN steps. Requires DIA-NN >= 2.3.2 (use `-profile diann_v2_3_2`). This is a beta feature with known limitations; see the usage documentation for details. |
 
 > **Note:** DDA support requires DIA-NN >= 2.3.2. Enable this profile with
@@ -134,29 +134,29 @@ in a Nextflow config file.
 
 ## InfinDIA (Experimental)
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
+| Parameter            | Type    | Default | Description                                                                            |
+| -------------------- | ------- | ------- | -------------------------------------------------------------------------------------- |
 | `--enable_infin_dia` | boolean | `false` | Enable InfinDIA for ultra-large search spaces. Requires DIA-NN >= 2.3.0. Experimental. |
-| `--diann_pre_select` | integer | `null` | Precursor limit (`--pre-select N`) for InfinDIA pre-search. |
+| `--diann_pre_select` | integer | `null`  | Precursor limit (`--pre-select N`) for InfinDIA pre-search.                            |
 
 > **Note:** InfinDIA requires DIA-NN >= 2.3.0 and is considered experimental.
 
 ## Quality Control
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--enable_pmultiqc` | boolean | `true` | Generate a pmultiqc proteomics QC report. |
-| `--pmultiqc_idxml_skip` | boolean | `true` | Skip idXML files (do not generate search engine score plots) in the pmultiqc report. |
-| `--contaminant_string` | string | `CONT` | Contaminant affix string used by pmultiqc to identify contaminant proteins. |
-| `--protein_level_fdr_cutoff` | number | `0.01` | Experiment-wide protein/protein-group-level FDR cutoff. |
+| Parameter                    | Type    | Default | Description                                                                          |
+| ---------------------------- | ------- | ------- | ------------------------------------------------------------------------------------ |
+| `--enable_pmultiqc`          | boolean | `true`  | Generate a pmultiqc proteomics QC report.                                            |
+| `--pmultiqc_idxml_skip`      | boolean | `true`  | Skip idXML files (do not generate search engine score plots) in the pmultiqc report. |
+| `--contaminant_string`       | string  | `CONT`  | Contaminant affix string used by pmultiqc to identify contaminant proteins.          |
+| `--protein_level_fdr_cutoff` | number  | `0.01`  | Experiment-wide protein/protein-group-level FDR cutoff.                              |
 
 ## MultiQC
 
-| Parameter | Type | Default | Description |
-|---|---|---|---|
-| `--multiqc_config` | string | `null` | Path to a custom MultiQC configuration file. |
-| `--multiqc_title` | string | `null` | Custom title for the MultiQC report. Used as page header and default filename. |
-| `--multiqc_logo` | string | `null` | Path to a custom logo file for the MultiQC report. Must also be set in the MultiQC config. |
-| `--skip_table_plots` | boolean | `false` | Skip protein/peptide table plots in pmultiqc. Useful for very large datasets. |
-| `--max_multiqc_email_size` | string | `25.MB` | Maximum file size for MultiQC report attachments in summary emails. |
-| `--multiqc_methods_description` | string | `null` | Path to a custom YAML file containing an HTML methods description for MultiQC. |
+| Parameter                       | Type    | Default | Description                                                                                |
+| ------------------------------- | ------- | ------- | ------------------------------------------------------------------------------------------ |
+| `--multiqc_config`              | string  | `null`  | Path to a custom MultiQC configuration file.                                               |
+| `--multiqc_title`               | string  | `null`  | Custom title for the MultiQC report. Used as page header and default filename.             |
+| `--multiqc_logo`                | string  | `null`  | Path to a custom logo file for the MultiQC report. Must also be set in the MultiQC config. |
+| `--skip_table_plots`            | boolean | `false` | Skip protein/peptide table plots in pmultiqc. Useful for very large datasets.              |
+| `--max_multiqc_email_size`      | string  | `25.MB` | Maximum file size for MultiQC report attachments in summary emails.                        |
+| `--multiqc_methods_description` | string  | `null`  | Path to a custom YAML file containing an HTML methods description for MultiQC.             |

From 2cb774081933689b343f320b7a8ea9e6ac1d6c91 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 18:38:34 +0100
Subject: [PATCH 13/28] chore: remove internal planning doc to resolve merge
 conflict

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 docs/v1-release-roadmap.md | 282 -------------------------------------
 1 file changed, 282 deletions(-)
 delete mode 100644 docs/v1-release-roadmap.md

diff --git a/docs/v1-release-roadmap.md b/docs/v1-release-roadmap.md
deleted file mode 100644
index 1961f20..0000000
--- a/docs/v1-release-roadmap.md
+++ /dev/null
@@ -1,282 +0,0 @@
-# quantmsdiann v1.0.0 Release Roadmap — Design Spec
-
-**Date:** 2026-04-03
-**Author:** Yasset Perez-Riverol + Claude
-**Status:** Approved
-**Issues covered:** #1, #2, #3, #5, #7, #9, #10, #15, #17
-
----
-
-## Overview
-
-Comprehensive pre-release work for quantmsdiann v1.0.0 covering robustness fixes, DDA support via DIA-NN 2.3.2, new feature parameters, and documentation. Four-week timeline.
-
-## Architecture
-
-No new workflows or modules. The existing `workflows/dia.nf` pipeline handles both DIA and DDA since DIA-NN uses the same steps with `--dda` appended. Default container stays 1.8.1; 2.3.2 is the "latest" option.
-
-```
-SDRF_PARSING -> FILE_PREPARATION -> INSILICO_LIBRARY -> PRELIMINARY_ANALYSIS ->
-ASSEMBLE_EMPIRICAL -> INDIVIDUAL_ANALYSIS -> FINAL_QUANTIFICATION -> DIANN_MSSTATS -> PMULTIQC
-```
-
-DDA parallelization is identical to DIA — per-file parallel for PRELIMINARY_ANALYSIS and INDIVIDUAL_ANALYSIS, synchronization points at ASSEMBLE_EMPIRICAL and FINAL_QUANTIFICATION. Confirmed by DIA-NN author in vdemichev/DiaNN#1727.
-
----
-
-## Week 1: Robustness Fixes
-
-### 1.1 Fix tee pipes masking failures
-
-Add `set -o pipefail` or `exit ${PIPESTATUS[0]}` to script blocks in:
-
-- `modules/local/diann/generate_cfg/main.nf`
-- `modules/local/diann/diann_msstats/main.nf`
-- `modules/local/samplesheet_check/main.nf`
-- `modules/local/sdrf_parsing/main.nf`
-
-**Risk:** Without this fix, if `quantmsutilsc` or `parse_sdrf` fails, the Nextflow task appears to succeed because `tee` returns exit code 0.
-
-### 1.2 Add error retry to long-running DIA-NN tasks
-
-Add `label 'error_retry'` to:
-
-- PRELIMINARY_ANALYSIS (process_high)
-- INDIVIDUAL_ANALYSIS (process_high)
-- FINAL_QUANTIFICATION (process_high)
-- INSILICO_LIBRARY_GENERATION (process_medium)
-- ASSEMBLE_EMPIRICAL_LIBRARY (process_medium)
-
-These are the longest-running tasks and most susceptible to transient failures (OOM, I/O timeouts).
-
-### 1.3 Empty input guards
-
-- `subworkflows/local/create_input_channel/main.nf` — Fail fast if SDRF has 0 data rows after `splitCsv`. Add a `.count()` check with error message.
-- `workflows/dia.nf` — Guard `.first()` calls on `ch_searchdb` and `ch_experiment_meta` with `.ifEmpty { error("...") }` to prevent indefinite hangs on empty inputs.
-
-### 1.4 New test configs
-
-**`conf/tests/test_dia_skip_preanalysis.config`:**
-
-- Sets `skip_preliminary_analysis = true`
-- Uses default `mass_acc_ms1`, `mass_acc_ms2`, `scan_window` params
-- Same PXD026600 test data as test_dia
-- Validates the skip path that is currently untested in CI
-
-**`conf/tests/test_dia_speclib.config`:**
-
-- Sets `diann_speclib` to a pre-built spectral library
-- Skips INSILICO_LIBRARY_GENERATION (the `if` branch in dia.nf line 55-56)
-- Requires a small test spectral library in quantms-test-datasets (or generated from existing test data)
-
-Both configs added to `extended_ci.yml` stage 2a.
-
----
-
-## Week 2: Container Build + DDA Support
-
-### 2.1 Container (PR to bigbio/quantms-containers)
-
-Build and push `ghcr.io/bigbio/diann:2.3.2` from existing Dockerfile at `quantms-containers/diann-2.3.2/Dockerfile`. The Dockerfile downloads `DIA-NN-2.3.2-Academia-Linux.zip` from the official GitHub release.
-
-### 2.2 Version config
-
-Add `conf/diann_versions/v2_3_2.config`:
-
-```groovy
-params.diann_version = '2.3.2'
-process {
-    withLabel: diann {
-        container = 'ghcr.io/bigbio/diann:2.3.2'
-    }
-}
-singularity.enabled = false
-docker.enabled = true
-```
-
-Add profile in `nextflow.config`:
-
-```groovy
-diann_v2_3_2 { includeConfig 'conf/diann_versions/v2_3_2.config' }
-```
-
-### 2.3 DDA implementation
-
-**New param** in `nextflow.config`:
-
-```groovy
-diann_dda = false  // Enable DDA analysis mode (requires DIA-NN >= 2.3.2)
-```
-
-**Version guard** in `workflows/dia.nf` at workflow start:
-
-```groovy
-if (params.diann_dda && params.diann_version < '2.3.2') {
-    error("DDA mode requires DIA-NN >= 2.3.2. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
-}
-```
-
-**Pass `--dda` to all DIA-NN modules** — In each module's script block, add:
-
-```groovy
-diann_dda_flag = params.diann_dda ? "--dda" : ""
-```
-
-And append `${diann_dda_flag}` to the DIA-NN command. Add `'--dda'` to the `blocked` list in all 5 modules.
-
-**Accept DDA in create_input_channel** — Modify `create_input_channel/main.nf` lines 78-88:
-
-```groovy
-if (acqMethod.toLowerCase().contains("data-independent acquisition") || acqMethod.toLowerCase().contains("dia")) {
-    meta.acquisition_method = "dia"
-} else if (params.diann_dda && (acqMethod.toLowerCase().contains("data-dependent acquisition") || acqMethod.toLowerCase().contains("dda"))) {
-    meta.acquisition_method = "dda"
-} else if (acqMethod.isEmpty()) {
-    meta.acquisition_method = params.diann_dda ? "dda" : "dia"
-} else {
-    log.error("Unsupported acquisition method: '${acqMethod}'. ...")
-    exit(1)
-}
-```
-
-### 2.4 Test data (PR to bigbio/quantms-test-datasets)
-
-Add `comment[proteomics data acquisition method]` column with value `NT=Data-Dependent Acquisition;AC=PRIDE:0000627` to `testdata/lfq_ci/BSA/BSA_design.sdrf.tsv`. The sdrf-pipelines `convert-diann` already extracts this column correctly — no sdrf-pipelines changes needed.
-
-### 2.5 Test config
-
-**`conf/tests/test_dda.config`:**
-
-- Points to BSA dataset from `bigbio/quantms-test-datasets/testdata/lfq_ci/BSA/`
-- Sets `diann_dda = true`
-- Pins to `ghcr.io/bigbio/diann:2.3.2`
-- Added to `extended_ci.yml` stage 2a (private containers)
-
-### 2.6 Schema + blocked list
-
-- Add `diann_dda` to `nextflow_schema.json` with description and version note
-- Add `'--dda'` to blocked lists in all 5 DIA-NN modules
-
----
-
-## Week 3: Features
-
-### 3.1 New DIA-NN parameters
-
-| Parameter              | Flag               | Min Version | Module                      | Default         |
-| ---------------------- | ------------------ | ----------- | --------------------------- | --------------- |
-| `diann_light_models`   | `--light-models`   | 2.0         | INSILICO_LIBRARY_GENERATION | false           |
-| `diann_export_quant`   | `--export-quant`   | 2.0         | FINAL_QUANTIFICATION        | false           |
-| `diann_read_threads`   | `--read-threads N` | 2.0         | All DIA-NN steps            | null (disabled) |
-| `diann_site_ms1_quant` | `--site-ms1-quant` | 2.0         | FINAL_QUANTIFICATION        | false           |
-
-Each parameter: add to `nextflow.config`, `nextflow_schema.json`, module script block (with version guard where needed), and module blocked list.
-
-### 3.2 InfinDIA groundwork (issue #10)
-
-New params:
-
-- `enable_infin_dia` (boolean, default: false) — requires >= 2.3.0
-- `diann_pre_select` (integer, optional) — `--pre-select N` precursor limit
-
-Implementation:
-
-- Pass `--infin-dia` to INSILICO_LIBRARY_GENERATION when enabled
-- Version guard: error if enabled with DIA-NN < 2.3.0
-- No test config — InfinDIA needs large databases to be meaningful
-- Document as experimental/advanced feature
-
-### 3.3 Close resolved issues
-
-- **#17** (phospho monitor-mod) — Already implemented via `diann_config.cfg` extraction. Close with explanation.
-- **#2** (param consolidation) — Superseded by #4 (Phase 6). Close as duplicate.
-- **#3** (ext.args documentation) — Close with documentation update in Week 4.
-
----
-
-## Week 4: Documentation
-
-### 4.1 Create `docs/parameters.md`
-
-Comprehensive parameter reference with all ~70 params grouped by:
-
-- Input/output options
-- File preparation (conversion, indexing, statistics)
-- DIA-NN general settings
-- Mass accuracy and calibration
-- Library generation
-- Quantification and output
-- DDA mode
-- InfinDIA (experimental)
-- Quality control (pmultiqc)
-- MultiQC options
-- Boilerplate (nf-core standard)
-
-Each param: name, type, default, description, version requirement (if any).
-
-### 4.2 Complete `docs/usage.md`
-
-Add missing sections:
-
-- Preprocessing params (`reindex_mzml`, `mzml_statistics`, `convert_dotd`)
-- QC params (`enable_pmultiqc`, `skip_table_plots`, `contaminant_string`)
-- MultiQC options
-- DDA mode with limitations
-- InfinDIA (basic)
-- `diann_extra_args` scope per module (closes #3)
-- `--verbose_modules` profile
-- Container version override guide (closes #9)
-- Singularity usage with image caching
-- SLURM example (from `pride_codon_slurm.config`)
-- AWS/cloud basics (Wave profile)
-
-### 4.3 Update `docs/output.md`
-
-- Intermediate outputs under `--verbose_modules`
-- Parquet vs TSV output explanation (DIA-NN 2.0+)
-- MSstats format section
-
-### 4.4 Housekeeping
-
-- Add pmultiqc to `CITATIONS.md`
-- Fix #15 (docs mismatch for `--input`)
-- Update README with DIA-NN version table and link to parameter reference
-- Close #1 (documentation issue), #9 (container docs), #15 (input mismatch)
-
----
-
-## Issues Status After Release
-
-| Issue | Status           | Resolution                                           |
-| ----- | ---------------- | ---------------------------------------------------- |
-| #1    | Closed           | Parameter documentation created                      |
-| #2    | Closed           | Superseded by #4                                     |
-| #3    | Closed           | ext.args scope documented                            |
-| #5    | Closed           | DDA support implemented                              |
-| #7    | Closed           | Phase 2 features wired                               |
-| #9    | Closed           | Container docs added                                 |
-| #10   | Partially closed | InfinDIA groundwork done, full support needs testing |
-| #15   | Closed           | Docs mismatch fixed                                  |
-| #17   | Closed           | Already implemented                                  |
-| #4    | Open             | Blocked on sdrf-pipelines converter release          |
-| #6    | Open             | Blocked on PRIDE ontology release                    |
-| #25   | Open             | QPX deferred to next release                         |
-
----
-
-## External PRs Required
-
-1. **bigbio/quantms-containers** — Build and push `ghcr.io/bigbio/diann:2.3.2`
-2. **bigbio/quantms-test-datasets** — Add `comment[proteomics data acquisition method]` column to BSA SDRF
-
----
-
-## Success Criteria
-
-- `nf-core pipelines lint --release` passes with 0 failures
-- `pre-commit run --all-files` passes
-- All existing CI tests still pass (test_dia, test_dia_dotd, etc.)
-- New tests pass: test_dia_skip_preanalysis, test_dia_speclib, test_dda
-- DDA test completes with BSA dataset on DIA-NN 2.3.2
-- `docs/parameters.md` covers all params in `nextflow_schema.json`
-- `docs/usage.md` covers all major use cases

From 046c7a1e1ce1d544ad7ae8ce20545c4c110bf025 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 18:42:22 +0100
Subject: [PATCH 14/28] fix: address PR #32 review comments

- Add version guard for DIA-NN 2.0+ params (--light-models,
  --export-quant, --site-ms1-quant) to prevent crashes with 1.8.1
- Add *.site_report.parquet as optional output in FINAL_QUANTIFICATION
  for site-level PTM quantification

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 modules/local/diann/final_quantification/main.nf | 1 +
 workflows/dia.nf                                 | 9 +++++++++
 2 files changed, 10 insertions(+)

diff --git a/modules/local/diann/final_quantification/main.nf b/modules/local/diann/final_quantification/main.nf
index fc8bbd0..0c14f9a 100644
--- a/modules/local/diann/final_quantification/main.nf
+++ b/modules/local/diann/final_quantification/main.nf
@@ -35,6 +35,7 @@ process FINAL_QUANTIFICATION {
     // Different library files format are exported due to different DIA-NN versions
     path "empirical_library.tsv", emit: final_speclib, optional: true
     path "empirical_library.tsv.skyline.speclib", emit: skyline_speclib, optional: true
+    path "*.site_report.parquet", emit: site_report, optional: true
     path "versions.yml", emit: versions
 
     when:
diff --git a/workflows/dia.nf b/workflows/dia.nf
index 899d226..635295a 100644
--- a/workflows/dia.nf
+++ b/workflows/dia.nf
@@ -46,6 +46,15 @@ workflow DIA {
         error("InfinDIA requires DIA-NN >= 2.3.0. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
     }
 
+    // Version guard for DIA-NN 2.0+ features
+    if ((params.diann_light_models || params.diann_export_quant || params.diann_site_ms1_quant) && params.diann_version < '2.0') {
+        def enabled = []
+        if (params.diann_light_models) enabled << '--light-models'
+        if (params.diann_export_quant) enabled << '--export-quant'
+        if (params.diann_site_ms1_quant) enabled << '--site-ms1-quant'
+        error("${enabled.join(', ')} require DIA-NN >= 2.0. Current version: ${params.diann_version}. Use -profile diann_v2_1_0 or later")
+    }
+
     ch_searchdb = channel.fromPath(params.database, checkIfExists: true)
         .ifEmpty { error("No protein database found at '${params.database}'. Provide --database <path/to/proteins.fasta>") }
         .first()

From 1a3610a7680300fa310408a2b3ed03de63391372 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Fri, 3 Apr 2026 18:54:11 +0100
Subject: [PATCH 15/28] =?UTF-8?q?fix:=20critical=20DDA=20bugs=20=E2=80=94?=
 =?UTF-8?q?=20missing=20version=20param=20and=20channel=20routing?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

1. test_dda.config: Add diann_version = '2.3.2' so the version guard
   doesn't reject DDA mode (default is 1.8.1, guard requires >= 2.3.2)

2. quantmsdiann.nf: Update branch condition to also match "dda"
   acquisition method. Previously "dda".contains("dia") was false,
   causing all DDA files to be silently dropped from processing.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 conf/tests/test_dda.config | 1 +
 workflows/quantmsdiann.nf  | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/tests/test_dda.config b/conf/tests/test_dda.config
index c0ebb24..d9d7896 100644
--- a/conf/tests/test_dda.config
+++ b/conf/tests/test_dda.config
@@ -31,6 +31,7 @@ params {
 
     // DDA mode
     diann_dda = true
+    diann_version = '2.3.2'
 
     // Search parameters matching BSA dataset
     min_peptide_length = 7
diff --git a/workflows/quantmsdiann.nf b/workflows/quantmsdiann.nf
index 9d869ac..0e31703 100644
--- a/workflows/quantmsdiann.nf
+++ b/workflows/quantmsdiann.nf
@@ -64,7 +64,7 @@ workflow QUANTMSDIANN {
 
     FILE_PREPARATION.out.results
         .branch { item ->
-            dia: item[0].acquisition_method.toLowerCase().contains("dia")
+            dia: item[0].acquisition_method.toLowerCase().contains("dia") || item[0].acquisition_method.toLowerCase().contains("dda")
         }
         .set { ch_fileprep_result }
     //

From 7a20d7dad90e228234bfe204f8db84d18e7b2c0c Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Sat, 4 Apr 2026 07:32:24 +0100
Subject: [PATCH 16/28] fix: make --no-ifs-removal and --no-main-report
 version-conditional

These flags exist in DIA-NN 1.8.x but were removed in 2.3.x, causing
'unrecognised option' warnings. Only pass them for versions < 2.3.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 modules/local/diann/individual_analysis/main.nf | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/modules/local/diann/individual_analysis/main.nf b/modules/local/diann/individual_analysis/main.nf
index 1e24905..4371b9c 100644
--- a/modules/local/diann/individual_analysis/main.nf
+++ b/modules/local/diann/individual_analysis/main.nf
@@ -84,6 +84,10 @@ process INDIVIDUAL_ANALYSIS {
     diann_im_window = params.diann_im_window ? "--im-window $params.diann_im_window" : ""
     diann_dda_flag = params.diann_dda ? "--dda" : ""
 
+    // Flags removed in DIA-NN 2.3.x — only pass for older versions
+    no_ifs_removal = params.diann_version < '2.3' ? "--no-ifs-removal" : ""
+    no_main_report = params.diann_version < '2.3' ? "--no-main-report" : ""
+
     // Per-file scan ranges from SDRF (empty = no flag, DIA-NN auto-detects)
     min_pr_mz = meta['ms1minmz'] ? "--min-pr-mz ${meta['ms1minmz']}" : ""
     max_pr_mz = meta['ms1maxmz'] ? "--max-pr-mz ${meta['ms1maxmz']}" : ""
@@ -103,8 +107,8 @@ process INDIVIDUAL_ANALYSIS {
             --mass-acc ${mass_acc_ms2} \\
             --mass-acc-ms1 ${mass_acc_ms1} \\
             --window ${scan_window} \\
-            --no-ifs-removal \\
-            --no-main-report \\
+            ${no_ifs_removal} \\
+            ${no_main_report} \\
             --relaxed-prot-inf \\
             --pg-level $params.pg_level \\
             ${min_pr_mz} \\

From 1a929ae854862e27efda47663ee008b6c50be40b Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 6 Apr 2026 14:04:41 +0100
Subject: [PATCH 17/28] docs: update Zenodo DOI to 10.5281/zenodo.19437128

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 67c2de6..99ef33d 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
 
 [![GitHub Actions CI Status](https://github.com/bigbio/quantmsdiann/actions/workflows/ci.yml/badge.svg)](https://github.com/bigbio/quantmsdiann/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/bigbio/quantmsdiann/actions/workflows/linting.yml/badge.svg)](https://github.com/bigbio/quantmsdiann/actions/workflows/linting.yml)
-[![Cite with Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.15573386.svg)](https://doi.org/10.5281/zenodo.15573386)
+[![Cite with Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.19437128.svg)](https://doi.org/10.5281/zenodo.19437128)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
@@ -103,7 +103,7 @@ If you would like to contribute to this pipeline, please see the [contributing g
 
 If you use quantmsdiann in your research, please cite:
 
-> Dai et al. "quantms: a cloud-based pipeline for quantitative proteomics" (2024). DOI: [10.5281/zenodo.15573386](https://doi.org/10.5281/zenodo.15573386)
+> Dai et al. "quantms: a cloud-based pipeline for quantitative proteomics" (2024). DOI: [10.5281/zenodo.19437128](https://doi.org/10.5281/zenodo.19437128)
 
 An extensive list of references for the tools used by the pipeline can be found in the [CITATIONS.md](CITATIONS.md) file.
 

From bd80512dd91f51564f1cf96a17da533ec074c341 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 6 Apr 2026 21:10:20 +0100
Subject: [PATCH 18/28] fix: remove tdf2mzml module and references from
 documentation

Bruker .d to mzML conversion via tdf2mzml is no longer needed.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 AGENTS.md                                    |  4 +-
 README.md                                    |  2 +-
 modules/local/utils/tdf2mzml/main.nf         | 38 ------------------
 modules/local/utils/tdf2mzml/meta.yml        | 42 --------------------
 subworkflows/local/file_preparation/meta.yml |  1 -
 5 files changed, 3 insertions(+), 84 deletions(-)
 delete mode 100644 modules/local/utils/tdf2mzml/main.nf
 delete mode 100644 modules/local/utils/tdf2mzml/meta.yml

diff --git a/AGENTS.md b/AGENTS.md
index 2c32d31..982fcfe 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -80,7 +80,7 @@ quantmsdiann/
 │   ├── pmultiqc/              # QC reporting
 │   ├── sdrf_parsing/          # SDRF parsing
 │   ├── samplesheet_check/     # Input validation
-│   └── utils/                 # tdf2mzml, decompress, mzml stats
+│   └── utils/                 # decompress, mzml stats
 ├── conf/
 │   ├── base.config            # Resource definitions
 │   ├── modules/               # Module-specific configs
@@ -97,7 +97,7 @@ quantmsdiann/
 The pipeline executes the following steps:
 
 1. **SDRF Validation & Parsing** - Validates input SDRF and extracts metadata
-2. **File Preparation** - Converts RAW/mzML/.d/.dia files (ThermoRawFileParser, tdf2mzml)
+2. **File Preparation** - Converts RAW/mzML/.d/.dia files (ThermoRawFileParser)
 3. **Generate Config** - Creates DIA-NN config from enzyme/modifications (`quantmsutilsc dianncfg`)
 4. **In-Silico Library Generation** - Predicts spectral library from FASTA (or uses provided library)
 5. **Preliminary Analysis** - Per-file calibration and mass accuracy determination
diff --git a/README.md b/README.md
index 99ef33d..ee88b0e 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
 The pipeline takes [SDRF](https://github.com/bigbio/proteomics-metadata-standard) metadata and mass spectrometry data files (`.raw`, `.mzML`, `.d`, `.dia`) as input and performs:
 
 1. **Input validation** — SDRF parsing and validation via [sdrf-pipelines](https://github.com/bigbio/sdrf-pipelines)
-2. **File preparation** — RAW to mzML conversion ([ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser)), indexing, Bruker `.d` handling ([tdf2mzml](https://github.com/bigbio/tdf2mzml))
+2. **File preparation** — RAW to mzML conversion ([ThermoRawFileParser](https://github.com/compomics/ThermoRawFileParser)), indexing
 3. **In-silico spectral library generation** — deep learning-based prediction, or use a user-provided library (`--diann_speclib`)
 4. **Preliminary analysis** — per-file calibration and mass accuracy estimation (parallelized)
 5. **Empirical library assembly** — consensus library from preliminary results with RT profiling
diff --git a/modules/local/utils/tdf2mzml/main.nf b/modules/local/utils/tdf2mzml/main.nf
deleted file mode 100644
index a242935..0000000
--- a/modules/local/utils/tdf2mzml/main.nf
+++ /dev/null
@@ -1,38 +0,0 @@
-process TDF2MZML {
-    tag "$meta.id"
-    label 'process_single'
-    label 'error_retry'
-
-    container 'quay.io/bigbio/tdf2mzml:latest' // TODO: pin to a specific version tag for reproducibility
-
-    input:
-    tuple val(meta), path(rawfile)
-
-    output:
-    tuple val(meta), path("*.mzML"), emit: mzmls_converted
-    path "versions.yml",   emit: versions
-    path "*.log",   emit: log
-
-    script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    """
-    echo "Converting..." | tee --append ${rawfile.baseName}_conversion.log
-    tdf2mzml.py -i *.d $args 2>&1 | tee --append ${rawfile.baseName}_conversion.log
-
-    # Rename .mzml to .mzML via temp file to handle case-insensitive filesystems (e.g. macOS)
-    mv *.mzml __tmp_converted.mzML && mv __tmp_converted.mzML ${file(rawfile.baseName).baseName}.mzML
-
-    # Rename .d directory only if the name differs (avoid 'same file' error)
-    target_d="${file(rawfile.baseName).baseName}.d"
-    if [ ! -d "\${target_d}" ]; then
-        mv *.d "\${target_d}"
-    fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        tdf2mzml.py: \$(tdf2mzml.py --version)
-    END_VERSIONS
-    """
-}
diff --git a/modules/local/utils/tdf2mzml/meta.yml b/modules/local/utils/tdf2mzml/meta.yml
deleted file mode 100644
index ebb90b8..0000000
--- a/modules/local/utils/tdf2mzml/meta.yml
+++ /dev/null
@@ -1,42 +0,0 @@
-name: tdf2mzml
-description: convert raw bruker files to mzml files
-keywords:
-  - raw
-  - mzML
-  - .d
-tools:
-  - tdf2mzml:
-      description: |
-        It takes a bruker .d raw file as input and outputs indexed mzML
-      homepage: https://github.com/mafreitas/tdf2mzml
-      documentation: https://github.com/mafreitas/tdf2mzml
-input:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-  - rawfile:
-      type: file
-      description: |
-        Bruker .d raw directory
-      pattern: "*.d"
-output:
-  - meta:
-      type: map
-      description: |
-        Groovy Map containing sample information
-        e.g. [ id:'MD5', enzyme:trypsin ]
-  - mzml:
-      type: file
-      description: indexed mzML
-      pattern: "*.mzML"
-  - log:
-      type: file
-      description: log file
-      pattern: "*.log"
-  - version:
-      type: file
-      description: File containing software version
-      pattern: "versions.yml"
-authors:
-  - "@jspaezp"
diff --git a/subworkflows/local/file_preparation/meta.yml b/subworkflows/local/file_preparation/meta.yml
index 54211c7..54d34fc 100644
--- a/subworkflows/local/file_preparation/meta.yml
+++ b/subworkflows/local/file_preparation/meta.yml
@@ -8,7 +8,6 @@ keywords:
   - proteomics
 components:
   - thermorawfileparser
-  - tdf2mzml
   - decompress
   - mzml/indexing
   - mzml/statistics

From 66ece2699e848d80504da562c38a7cd6d1d8f628 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Mon, 6 Apr 2026 21:12:31 +0100
Subject: [PATCH 19/28] chore: bump version to 1.0.1dev for next release cycle

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 33c5c95..fe29615 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -362,7 +362,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=25.04.0'
-    version         = '1.0.0'
+    version         = '1.0.1dev'
     doi             = '10.5281/zenodo.15573386'
 }
 

From 1dd2786a5dcff7ebeb385dfa97f8dbc8870bdb91 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Tue, 7 Apr 2026 07:24:21 +0100
Subject: [PATCH 20/28] style: fix prettier formatting in parameters.md

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 docs/parameters.md | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/docs/parameters.md b/docs/parameters.md
index b95bdd1..0a3eac8 100644
--- a/docs/parameters.md
+++ b/docs/parameters.md
@@ -58,10 +58,10 @@ This document lists every pipeline parameter organised by category. Default valu
 | `--diann_debug`          | integer | `3`     | DIA-NN debug/verbosity level (0-4). Higher values produce more verbose logs.                                                                                                                                 |
 | `--diann_speclib`        | string  | `null`  | Path to an external spectral library. If provided, the in-silico library generation step is skipped.                                                                                                         |
 | `--diann_extra_args`     | string  | `null`  | Extra arguments appended to all DIA-NN steps. Flags incompatible with a step are automatically stripped with a warning. See [Passing Extra Arguments to DIA-NN](usage.md#passing-extra-arguments-to-dia-nn). |
-| `--diann_dda`            | boolean | `false` | Enable DDA (Data-Dependent Acquisition) analysis mode. Passes `--dda` to all DIA-NN steps. Requires DIA-NN >= 2.3.2. Beta feature.                                                                          |
-| `--diann_light_models`   | boolean | `false` | Enable `--light-models` for 10x faster in-silico library generation. Requires DIA-NN >= 2.0.                                                                                                                |
-| `--diann_export_quant`   | boolean | `false` | Enable `--export-quant` for fragment-level parquet data export. Requires DIA-NN >= 2.0.                                                                                                                     |
-| `--diann_site_ms1_quant` | boolean | `false` | Enable `--site-ms1-quant` to use MS1 apex intensities for PTM site quantification. Requires DIA-NN >= 2.0.                                                                                                  |
+| `--diann_dda`            | boolean | `false` | Enable DDA (Data-Dependent Acquisition) analysis mode. Passes `--dda` to all DIA-NN steps. Requires DIA-NN >= 2.3.2. Beta feature.                                                                           |
+| `--diann_light_models`   | boolean | `false` | Enable `--light-models` for 10x faster in-silico library generation. Requires DIA-NN >= 2.0.                                                                                                                 |
+| `--diann_export_quant`   | boolean | `false` | Enable `--export-quant` for fragment-level parquet data export. Requires DIA-NN >= 2.0.                                                                                                                      |
+| `--diann_site_ms1_quant` | boolean | `false` | Enable `--site-ms1-quant` to use MS1 apex intensities for PTM site quantification. Requires DIA-NN >= 2.0.                                                                                                   |
 
 ## 6. Mass Accuracy & Calibration
 
@@ -102,8 +102,8 @@ This document lists every pipeline parameter organised by category. Default valu
 | `--skip_preliminary_analysis` | boolean | `false` | Skip preliminary analysis. Use the provided spectral library as-is instead of generating a local consensus library.                  |
 | `--empirical_assembly_log`    | string  | `null`  | Path to a pre-existing empirical assembly log file. Only used when `--skip_preliminary_analysis true` and `--diann_speclib` are set. |
 | `--random_preanalysis`        | boolean | `false` | Enable random selection of spectrum files for empirical library generation.                                                          |
-| `--random_preanalysis_seed`   | integer | `42`    | Random seed for file selection when `--random_preanalysis` is enabled.                                                              |
-| `--empirical_assembly_ms_n`   | integer | `200`   | Number of randomly selected spectrum files when `--random_preanalysis` is enabled.                                                  |
+| `--random_preanalysis_seed`   | integer | `42`    | Random seed for file selection when `--random_preanalysis` is enabled.                                                               |
+| `--empirical_assembly_ms_n`   | integer | `200`   | Number of randomly selected spectrum files when `--random_preanalysis` is enabled.                                                   |
 
 ## 11. Quantification & Output
 

From 9d9d44405e3d582269c982cdaa41d37d98244244 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Tue, 7 Apr 2026 08:52:06 +0100
Subject: [PATCH 21/28] fix: add GHCR login to CI for test_dda private
 container

The test_dda profile uses ghcr.io/bigbio/diann:2.3.2 which is a
private container requiring authentication. Add Docker login step
(matching merge_ci.yml) conditioned on test_dda profile.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .github/workflows/ci.yml | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 20bd668..aadf1dd 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -60,6 +60,15 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
+      - name: Log in to GitHub Container Registry
+        if: matrix.test_profile == 'test_dda'
+        env:
+          GHCR_TOKEN: ${{ secrets.GHCR_TOKEN }}
+        run: |
+          if [ -n "$GHCR_TOKEN" ]; then
+            echo "${{ secrets.GHCR_TOKEN }}" | docker login ghcr.io -u ${{ secrets.GHCR_USERNAME }} --password-stdin
+          fi
+
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@v1.3.1
 

From 5f716f61e2bb17866bc5c14249573466ff25a1d4 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Tue, 7 Apr 2026 09:17:15 +0100
Subject: [PATCH 22/28] fix: remove plan docs, add semantic version comparison
 utility

- Remove implementation plan from repo, add docs/plans/ to .gitignore
- Add lib/VersionUtils.groovy for semantic version comparison
  (prevents string comparison bugs like '2.10.0' < '2.3')
- Update all version guards in dia.nf and module scripts to use
  VersionUtils.versionLessThan/versionAtLeast

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .gitignore                                    |   1 +
 .../2026-04-03-v1-release-implementation.md   | 805 ------------------
 lib/VersionUtils.groovy                       |  34 +
 .../local/diann/final_quantification/main.nf  |   2 +-
 .../local/diann/individual_analysis/main.nf   |   4 +-
 workflows/dia.nf                              |   6 +-
 6 files changed, 41 insertions(+), 811 deletions(-)
 delete mode 100644 docs/plans/2026-04-03-v1-release-implementation.md
 create mode 100644 lib/VersionUtils.groovy

diff --git a/.gitignore b/.gitignore
index 52812e6..6a54d55 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,3 +21,4 @@ null/
 .codacy/
 .github/instructions/codacy.instructions.md
 docs/superpowers/
+docs/plans/
diff --git a/docs/plans/2026-04-03-v1-release-implementation.md b/docs/plans/2026-04-03-v1-release-implementation.md
deleted file mode 100644
index 8439513..0000000
--- a/docs/plans/2026-04-03-v1-release-implementation.md
+++ /dev/null
@@ -1,805 +0,0 @@
-# quantmsdiann v1.0.0 Release — Implementation Plan
-
-> **For agentic workers:** REQUIRED SUB-SKILL: Use superpowers:subagent-driven-development (recommended) or superpowers:executing-plans to implement this plan task-by-task. Steps use checkbox (`- [ ]`) syntax for tracking.
-
-**Goal:** Prepare quantmsdiann for a robust v1.0.0 release with DDA support, new DIA-NN parameters, and comprehensive documentation.
-
-**Architecture:** No new workflows or modules. All changes are additions to existing files — new params, flags, guards, test configs, and docs. DDA uses the same pipeline as DIA with `--dda` appended to all DIA-NN invocations. Default container stays 1.8.1; 2.3.2 is opt-in via profile.
-
-**Tech Stack:** Nextflow DSL2, nf-core, DIA-NN, Groovy, Bash
-
----
-
-## Task 1: Fix tee pipes masking failures
-
-**Files:**
-
-- Modify: `modules/local/diann/generate_cfg/main.nf:26`
-- Modify: `modules/local/diann/diann_msstats/main.nf:21-26`
-- Modify: `modules/local/samplesheet_check/main.nf:38-43`
-- Modify: `modules/local/sdrf_parsing/main.nf:24-30`
-
-- [ ] **Step 1: Add pipefail to generate_cfg**
-
-In `modules/local/diann/generate_cfg/main.nf`, find the `"""` opening the script block (line 20) and add `set -o pipefail` as the first line:
-
-````groovy
-    """
-    set -o pipefail
-    parse_sdrf generate-diann-cfg \\
-    ...
-    ```
-
-- [ ] **Step 2: Add pipefail to diann_msstats**
-
-In `modules/local/diann/diann_msstats/main.nf`, find the `"""` opening the script block (line 20) and add `set -o pipefail`:
-
-```groovy
-    """
-    set -o pipefail
-    quantmsutilsc diann2msstats \\
-    ...
-    ```
-
-- [ ] **Step 3: Add pipefail to samplesheet_check**
-
-In `modules/local/samplesheet_check/main.nf`, find the `"""` opening the script block and add `set -o pipefail`:
-
-```groovy
-    """
-    set -o pipefail
-    ...
-    ```
-
-- [ ] **Step 4: Add pipefail to sdrf_parsing**
-
-In `modules/local/sdrf_parsing/main.nf`, find the `"""` opening the script block (line 22) and add `set -o pipefail`:
-
-```groovy
-    """
-    set -o pipefail
-    parse_sdrf convert-diann \\
-    ...
-    ```
-
-- [ ] **Step 5: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-git add modules/local/diann/generate_cfg/main.nf modules/local/diann/diann_msstats/main.nf modules/local/samplesheet_check/main.nf modules/local/sdrf_parsing/main.nf
-git commit -m "fix: add pipefail to all modules with tee pipes
-
-Without pipefail, if the command before tee fails, tee returns 0 and
-the Nextflow task appears to succeed. This masked failures in
-generate_cfg, diann_msstats, samplesheet_check, and sdrf_parsing."
-````
-
----
-
-## Task 2: Add error retry to long-running DIA-NN tasks
-
-**Files:**
-
-- Modify: `modules/local/diann/preliminary_analysis/main.nf:3-4`
-- Modify: `modules/local/diann/individual_analysis/main.nf:3-4`
-- Modify: `modules/local/diann/final_quantification/main.nf:3-4`
-- Modify: `modules/local/diann/insilico_library_generation/main.nf:3-4`
-- Modify: `modules/local/diann/assemble_empirical_library/main.nf:3-4`
-
-- [ ] **Step 1: Add error_retry label to all 5 DIA-NN modules**
-
-In each file, add `label 'error_retry'` after the existing labels. For example, `preliminary_analysis/main.nf` currently has:
-
-```groovy
-    label 'process_high'
-    label 'diann'
-```
-
-Change to:
-
-```groovy
-    label 'process_high'
-    label 'diann'
-    label 'error_retry'
-```
-
-Do the same for:
-
-- `individual_analysis/main.nf` (after `label 'diann'`)
-- `final_quantification/main.nf` (after `label 'diann'`)
-- `insilico_library_generation/main.nf` (after `label 'diann'`)
-- `assemble_empirical_library/main.nf` (after `label 'diann'`)
-
-- [ ] **Step 2: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-git add modules/local/diann/preliminary_analysis/main.nf modules/local/diann/individual_analysis/main.nf modules/local/diann/final_quantification/main.nf modules/local/diann/insilico_library_generation/main.nf modules/local/diann/assemble_empirical_library/main.nf
-git commit -m "fix: add error_retry label to all DIA-NN analysis modules
-
-These are the longest-running tasks and most susceptible to transient
-failures (OOM, I/O timeouts). The error_retry label enables automatic
-retry on signal exits (130-145, 104, 175)."
-```
-
----
-
-## Task 3: Add empty input guards
-
-**Files:**
-
-- Modify: `workflows/dia.nf:38,46`
-
-- [ ] **Step 1: Guard ch_searchdb with ifEmpty**
-
-In `workflows/dia.nf`, line 38, change:
-
-```groovy
-    ch_searchdb = channel.fromPath(params.database, checkIfExists: true).first()
-```
-
-To:
-
-```groovy
-    ch_searchdb = channel.fromPath(params.database, checkIfExists: true)
-        .ifEmpty { error("No protein database found at '${params.database}'. Provide --database <path/to/proteins.fasta>") }
-        .first()
-```
-
-- [ ] **Step 2: Guard ch_experiment_meta with ifEmpty**
-
-In `workflows/dia.nf`, line 46, change:
-
-```groovy
-    ch_experiment_meta = ch_result.meta.unique { m -> m.experiment_id }.first()
-```
-
-To:
-
-```groovy
-    ch_experiment_meta = ch_result.meta.unique { m -> m.experiment_id }
-        .ifEmpty { error("No valid input files found after SDRF parsing. Check your SDRF file and input paths.") }
-        .first()
-```
-
-- [ ] **Step 3: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-git add workflows/dia.nf
-git commit -m "fix: add empty input guards to prevent silent pipeline hangs
-
-Guard ch_searchdb and ch_experiment_meta with ifEmpty to fail fast
-with clear error messages instead of hanging indefinitely."
-```
-
----
-
-## Task 4: Add DIA-NN 2.3.2 version config and profile
-
-**Files:**
-
-- Create: `conf/diann_versions/v2_3_2.config`
-- Modify: `nextflow.config:245-247` (profiles section)
-
-- [ ] **Step 1: Create v2_3_2.config**
-
-Create `conf/diann_versions/v2_3_2.config`:
-
-```groovy
-/*
- * DIA-NN 2.3.2 container override (private ghcr.io)
- * Latest release with DDA support and InfinDIA.
- */
-params.diann_version = '2.3.2'
-
-process {
-    withLabel: diann {
-        container = 'ghcr.io/bigbio/diann:2.3.2'
-    }
-}
-
-singularity.enabled = false
-docker.enabled = true
-```
-
-- [ ] **Step 2: Add profile to nextflow.config**
-
-In `nextflow.config`, after the `diann_v2_2_0` profile line (around line 247), add:
-
-```groovy
-    diann_v2_3_2        { includeConfig 'conf/diann_versions/v2_3_2.config'    }
-```
-
-- [ ] **Step 3: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-git add conf/diann_versions/v2_3_2.config nextflow.config
-git commit -m "feat: add DIA-NN 2.3.2 version config and profile
-
-Adds conf/diann_versions/v2_3_2.config with ghcr.io/bigbio/diann:2.3.2
-container. Use -profile diann_v2_3_2 to opt in. Default stays 1.8.1.
-Enables DDA support and InfinDIA features."
-```
-
----
-
-## Task 5: Implement DDA support — params, version guard, flag passthrough
-
-**Files:**
-
-- Modify: `nextflow.config:53-57` (DIA-NN general params)
-- Modify: `nextflow_schema.json` (DIA-NN section)
-- Modify: `workflows/dia.nf:35-38` (version guard)
-- Modify: `subworkflows/local/create_input_channel/main.nf:75-88` (acquisition method)
-- Modify: `modules/local/diann/insilico_library_generation/main.nf` (blocked list + flag)
-- Modify: `modules/local/diann/preliminary_analysis/main.nf` (blocked list + flag)
-- Modify: `modules/local/diann/assemble_empirical_library/main.nf` (blocked list + flag)
-- Modify: `modules/local/diann/individual_analysis/main.nf` (blocked list + flag)
-- Modify: `modules/local/diann/final_quantification/main.nf` (blocked list + flag)
-
-- [ ] **Step 1: Add diann_dda param to nextflow.config**
-
-In `nextflow.config`, after `diann_extra_args = null` (line 57), add:
-
-```groovy
-    diann_dda               = false  // Enable DDA analysis mode (requires DIA-NN >= 2.3.2)
-```
-
-- [ ] **Step 2: Add diann_dda to nextflow_schema.json**
-
-In `nextflow_schema.json`, in the DIA-NN section (inside `"$defs"` > appropriate group), add:
-
-```json
-"diann_dda": {
-    "type": "boolean",
-    "description": "Enable DDA (Data-Dependent Acquisition) analysis mode. Passes --dda to all DIA-NN steps. Requires DIA-NN >= 2.3.2 (use -profile diann_v2_3_2). Beta feature — only trust q-values, PEP, RT/IM, Ms1.Apex.Area. PTM localization unreliable with DDA.",
-    "fa_icon": "fas fa-flask",
-    "default": false
-}
-```
-
-Add `"diann_dda"` to the corresponding `"required"` or `"properties"` list in the appropriate group.
-
-- [ ] **Step 3: Add version guard in workflows/dia.nf**
-
-In `workflows/dia.nf`, at the start of the `main:` block (after line 37), add:
-
-```groovy
-    // Version guard for DDA mode
-    if (params.diann_dda && params.diann_version < '2.3.2') {
-        error("DDA mode (--diann_dda) requires DIA-NN >= 2.3.2. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
-    }
-```
-
-- [ ] **Step 4: Accept DDA acquisition method in create_input_channel**
-
-In `subworkflows/local/create_input_channel/main.nf`, replace lines 75-88 (the acquisition method validation block):
-
-```groovy
-    // Validate acquisition method
-    def acqMethod = row.AcquisitionMethod?.toString()?.trim() ?: ""
-    if (acqMethod.toLowerCase().contains("data-independent acquisition") || acqMethod.toLowerCase().contains("dia")) {
-        meta.acquisition_method = "dia"
-    } else if (params.diann_dda && (acqMethod.toLowerCase().contains("data-dependent acquisition") || acqMethod.toLowerCase().contains("dda"))) {
-        meta.acquisition_method = "dda"
-    } else if (acqMethod.isEmpty()) {
-        meta.acquisition_method = params.diann_dda ? "dda" : "dia"
-    } else {
-        log.error("Unsupported acquisition method: '${acqMethod}'. This pipeline supports DIA" + (params.diann_dda ? " and DDA (--diann_dda)" : "") + ". Found in file: ${filestr}")
-        exit(1)
-    }
-```
-
-- [ ] **Step 5: Add --dda flag to all 5 DIA-NN modules**
-
-For each of the 5 DIA-NN modules, make two changes:
-
-**a) Add `'--dda'` to the blocked list.** In each module's `def blocked = [...]`, add `'--dda'` to the array.
-
-**b) Add the flag variable and append it to the command.** In each module's script block, after the existing flag variables (before the `"""` shell block), add:
-
-```groovy
-    diann_dda_flag = params.diann_dda ? "--dda" : ""
-```
-
-Then append `${diann_dda_flag} \\` to the DIA-NN command, before `\${mod_flags}` (or before `$args` if no mod_flags).
-
-Apply to:
-
-- `modules/local/diann/insilico_library_generation/main.nf`
-- `modules/local/diann/preliminary_analysis/main.nf`
-- `modules/local/diann/assemble_empirical_library/main.nf`
-- `modules/local/diann/individual_analysis/main.nf`
-- `modules/local/diann/final_quantification/main.nf`
-
-- [ ] **Step 6: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-conda run -n nfcore nf-core pipelines lint --dir .
-git add nextflow.config nextflow_schema.json workflows/dia.nf subworkflows/local/create_input_channel/main.nf modules/local/diann/*/main.nf
-git commit -m "feat: add DDA support via --diann_dda flag (#5)
-
-- New param diann_dda (boolean, default: false)
-- Version guard: requires DIA-NN >= 2.3.2
-- Passes --dda to all 5 DIA-NN modules when enabled
-- Accepts DDA acquisition method in SDRF when diann_dda=true
-- Added --dda to blocked lists in all modules
-
-Closes #5"
-```
-
----
-
-## Task 6: Add DDA test config
-
-**Files:**
-
-- Create: `conf/tests/test_dda.config`
-- Modify: `.github/workflows/extended_ci.yml:110-191` (stage 2a)
-
-- [ ] **Step 1: Create test_dda.config**
-
-Create `conf/tests/test_dda.config`:
-
-```groovy
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for testing DDA analysis (requires DIA-NN >= 2.3.2)
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Tests DDA mode using the BSA dataset with --diann_dda flag.
-    Uses ghcr.io/bigbio/diann:2.3.2.
-
-    Use as follows:
-        nextflow run bigbio/quantmsdiann -profile test_dda,docker [--outdir <OUTDIR>]
-
-------------------------------------------------------------------------------------------------
-*/
-
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '12.GB',
-        time: '48.h'
-    ]
-}
-
-params {
-    config_profile_name        = 'Test profile for DDA analysis'
-    config_profile_description = 'DDA test using BSA dataset with DIA-NN 2.3.2.'
-
-    outdir = './results_dda'
-
-    // Input data — BSA DDA dataset
-    input = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/lfq_ci/BSA/BSA_design.sdrf.tsv'
-    database = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/lfq_ci/BSA/18Protein_SoCe_Tr_detergents_trace.fasta'
-
-    // DDA mode
-    diann_dda = true
-
-    // Search parameters matching BSA dataset
-    min_peptide_length = 7
-    max_peptide_length = 30
-    max_precursor_charge = 3
-    allowed_missed_cleavages = 1
-    diann_normalize = false
-    publish_dir_mode = 'symlink'
-    max_mods = 2
-}
-
-process {
-    withLabel: diann {
-        container = 'ghcr.io/bigbio/diann:2.3.2'
-    }
-}
-
-singularity.enabled = false
-docker.enabled = true
-```
-
-- [ ] **Step 2: Add test_dda profile to nextflow.config**
-
-In `nextflow.config`, after the `test_dia_2_2_0` profile line (around line 241), add:
-
-```groovy
-    test_dda            { includeConfig 'conf/tests/test_dda.config'           }
-```
-
-- [ ] **Step 3: Add test_dda to extended_ci.yml stage 2a**
-
-In `.github/workflows/extended_ci.yml`, in the `test-latest` job matrix (around line 120), add `"test_dda"` to the `test_profile` array:
-
-```yaml
-test_profile: ["test_latest_dia", "test_dia_quantums", "test_dia_parquet", "test_dda"]
-```
-
-- [ ] **Step 4: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-git add conf/tests/test_dda.config nextflow.config .github/workflows/extended_ci.yml
-git commit -m "test: add DDA test config using BSA dataset with DIA-NN 2.3.2
-
-Uses bigbio/quantms-test-datasets BSA LFQ dataset (~34 MB) with
-diann_dda=true pinned to ghcr.io/bigbio/diann:2.3.2. Added to
-extended_ci.yml stage 2a (private containers)."
-```
-
----
-
-## Task 7: Add test configs for skip_preliminary_analysis and speclib input
-
-**Files:**
-
-- Create: `conf/tests/test_dia_skip_preanalysis.config`
-- Modify: `nextflow.config` (profiles section)
-- Modify: `.github/workflows/extended_ci.yml` (stage 2a)
-
-- [ ] **Step 1: Create test_dia_skip_preanalysis.config**
-
-Create `conf/tests/test_dia_skip_preanalysis.config`:
-
-```groovy
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for testing skip_preliminary_analysis path
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Tests the pipeline with skip_preliminary_analysis=true, using default
-    mass accuracy parameters. Validates the untested code path in dia.nf.
-
-    Use as follows:
-        nextflow run bigbio/quantmsdiann -profile test_dia_skip_preanalysis,docker [--outdir <OUTDIR>]
-
-------------------------------------------------------------------------------------------------
-*/
-
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '12.GB',
-        time: '48.h'
-    ]
-}
-
-params {
-    config_profile_name        = 'Test profile for skip preliminary analysis'
-    config_profile_description = 'Tests skip_preliminary_analysis path with default mass accuracy params.'
-
-    outdir = './results_skip_preanalysis'
-
-    // Input data — same as test_dia
-    input = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/dia_ci/PXD026600.sdrf.tsv'
-    database = 'https://raw.githubusercontent.com/bigbio/quantms-test-datasets/quantms/testdata/dia_ci/REF_EColi_K12_UPS1_combined.fasta'
-    min_pr_mz = 350
-    max_pr_mz = 950
-    min_fr_mz = 500
-    max_fr_mz = 1500
-    min_peptide_length = 15
-    max_peptide_length = 30
-    max_precursor_charge = 3
-    allowed_missed_cleavages = 1
-    diann_normalize = false
-    publish_dir_mode = 'symlink'
-    max_mods = 2
-
-    // Skip preliminary analysis — use default mass accuracy params
-    skip_preliminary_analysis = true
-    mass_acc_ms2 = 15
-    mass_acc_ms1 = 15
-    scan_window = 8
-}
-```
-
-- [ ] **Step 2: Add profile to nextflow.config**
-
-After existing test profiles (around line 242), add:
-
-```groovy
-    test_dia_skip_preanalysis { includeConfig 'conf/tests/test_dia_skip_preanalysis.config' }
-```
-
-- [ ] **Step 3: Add to extended_ci.yml stage 2a**
-
-In the `test-latest` job matrix, add `"test_dia_skip_preanalysis"` to the `test_profile` array.
-
-- [ ] **Step 4: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-git add conf/tests/test_dia_skip_preanalysis.config nextflow.config .github/workflows/extended_ci.yml
-git commit -m "test: add test config for skip_preliminary_analysis path
-
-Tests the previously untested code path where preliminary analysis is
-skipped and default mass accuracy parameters are used directly."
-```
-
----
-
-## Task 8: Add new DIA-NN feature parameters (light-models, export-quant, site-ms1-quant)
-
-**Files:**
-
-- Modify: `nextflow.config` (params section)
-- Modify: `nextflow_schema.json`
-- Modify: `modules/local/diann/insilico_library_generation/main.nf` (light-models)
-- Modify: `modules/local/diann/final_quantification/main.nf` (export-quant, site-ms1-quant)
-
-- [ ] **Step 1: Add params to nextflow.config**
-
-In `nextflow.config`, in the DIA-NN general section (after `diann_dda`, around line 58), add:
-
-```groovy
-    diann_light_models      = false  // add '--light-models' for 10x faster library generation (DIA-NN >= 2.0)
-    diann_export_quant      = false  // add '--export-quant' for fragment-level parquet export (DIA-NN >= 2.0)
-    diann_site_ms1_quant    = false  // add '--site-ms1-quant' for MS1 apex PTM quantification (DIA-NN >= 2.0)
-```
-
-- [ ] **Step 2: Add params to nextflow_schema.json**
-
-Add each param to the DIA-NN section in the schema with type, description, default, and fa_icon.
-
-- [ ] **Step 3: Wire --light-models in insilico_library_generation**
-
-In `modules/local/diann/insilico_library_generation/main.nf`:
-
-a) Add `'--light-models'` to the blocked list (line 26-32).
-
-b) After `diann_no_peptidoforms` variable (line 47), add:
-
-```groovy
-    diann_light_models = params.diann_light_models ? "--light-models" : ""
-```
-
-c) Append `${diann_light_models} \\` to the DIA-NN command before `${met_excision}`.
-
-- [ ] **Step 4: Wire --export-quant and --site-ms1-quant in final_quantification**
-
-In `modules/local/diann/final_quantification/main.nf`:
-
-a) Add `'--export-quant'` and `'--site-ms1-quant'` to the blocked list (line 45-50).
-
-b) After `diann_dda_flag` variable, add:
-
-```groovy
-    diann_export_quant = params.diann_export_quant ? "--export-quant" : ""
-    diann_site_ms1_quant = params.diann_site_ms1_quant ? "--site-ms1-quant" : ""
-```
-
-c) Append both to the DIA-NN command before `\${mod_flags}`.
-
-- [ ] **Step 5: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-conda run -n nfcore nf-core pipelines lint --dir .
-git add nextflow.config nextflow_schema.json modules/local/diann/insilico_library_generation/main.nf modules/local/diann/final_quantification/main.nf
-git commit -m "feat: add --light-models, --export-quant, --site-ms1-quant params (#7)
-
-- diann_light_models: 10x faster in-silico library generation
-- diann_export_quant: fragment-level parquet export
-- diann_site_ms1_quant: MS1 apex intensities for PTM quantification
-All require DIA-NN >= 2.0."
-```
-
----
-
-## Task 9: Add InfinDIA groundwork
-
-**Files:**
-
-- Modify: `nextflow.config` (params section)
-- Modify: `nextflow_schema.json`
-- Modify: `workflows/dia.nf` (version guard)
-- Modify: `modules/local/diann/insilico_library_generation/main.nf` (flag)
-
-- [ ] **Step 1: Add InfinDIA params to nextflow.config**
-
-After the DDA param, add:
-
-```groovy
-    // DIA-NN: InfinDIA (experimental, v2.3.0+)
-    enable_infin_dia        = false  // Enable InfinDIA for ultra-large search spaces
-    diann_pre_select        = null   // --pre-select N precursor limit for InfinDIA
-```
-
-- [ ] **Step 2: Add to nextflow_schema.json**
-
-Add `enable_infin_dia` (boolean) and `diann_pre_select` (integer, optional) to the schema.
-
-- [ ] **Step 3: Add version guard in workflows/dia.nf**
-
-After the DDA version guard, add:
-
-```groovy
-    if (params.enable_infin_dia && params.diann_version < '2.3.0') {
-        error("InfinDIA requires DIA-NN >= 2.3.0. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
-    }
-```
-
-- [ ] **Step 4: Wire flags in insilico_library_generation**
-
-In `modules/local/diann/insilico_library_generation/main.nf`:
-
-a) Add `'--infin-dia'` and `'--pre-select'` to the blocked list.
-
-b) Add flag variables:
-
-```groovy
-    infin_dia_flag = params.enable_infin_dia ? "--infin-dia" : ""
-    pre_select_flag = params.diann_pre_select ? "--pre-select $params.diann_pre_select" : ""
-```
-
-c) Append both to the DIA-NN command.
-
-- [ ] **Step 5: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-conda run -n nfcore nf-core pipelines lint --dir .
-git add nextflow.config nextflow_schema.json workflows/dia.nf modules/local/diann/insilico_library_generation/main.nf
-git commit -m "feat: add InfinDIA groundwork — enable_infin_dia param (#10)
-
-Experimental support for InfinDIA (DIA-NN 2.3.0+). Passes --infin-dia
-to library generation when enabled. Version guard enforces >= 2.3.0.
-No test config — InfinDIA requires large databases."
-```
-
----
-
-## Task 10: Documentation — parameters.md
-
-**Files:**
-
-- Create: `docs/parameters.md`
-
-- [ ] **Step 1: Create comprehensive parameter reference**
-
-Create `docs/parameters.md` with all params from `nextflow_schema.json` grouped by category. Read `nextflow.config` and `nextflow_schema.json` to get every param, its type, default, and description. Group into:
-
-1. Input/output options
-2. File preparation
-3. DIA-NN general
-4. Mass accuracy and calibration
-5. Library generation
-6. Quantification and output
-7. DDA mode
-8. InfinDIA (experimental)
-9. Quality control
-10. MultiQC options
-11. Boilerplate
-
-Each param entry: `| name | type | default | description |`
-
-- [ ] **Step 2: Commit**
-
-```bash
-git add docs/parameters.md
-git commit -m "docs: add comprehensive parameter reference (#1)
-
-Complete reference for all ~70 pipeline parameters grouped by category
-with types, defaults, descriptions, and version requirements.
-
-Closes #1"
-```
-
----
-
-## Task 11: Documentation — complete usage.md and output.md
-
-**Files:**
-
-- Modify: `docs/usage.md`
-- Modify: `docs/output.md`
-- Modify: `CITATIONS.md`
-- Modify: `README.md`
-
-- [ ] **Step 1: Add DDA section to usage.md**
-
-Add a "DDA Analysis Mode" section after the Bruker/timsTOF section with:
-
-- How to enable (`--diann_dda true -profile diann_v2_3_2`)
-- Limitations (beta, trusted columns only, PTM unreliable, MBR limited)
-- Example command
-- Link to DIA-NN DDA documentation
-
-- [ ] **Step 2: Add missing param sections to usage.md**
-
-Add sections for:
-
-- Preprocessing params (`reindex_mzml`, `mzml_statistics`, `convert_dotd`)
-- QC params (`enable_pmultiqc`, `skip_table_plots`, `contaminant_string`)
-- `diann_extra_args` scope per module
-- `--verbose_modules` profile
-- Container version override guide (DIA-NN version profiles)
-- Singularity usage
-- SLURM example
-
-- [ ] **Step 3: Update output.md**
-
-Add:
-
-- Parquet vs TSV output explanation
-- MSstats format section
-- Intermediate outputs under `--verbose_modules`
-
-- [ ] **Step 4: Add pmultiqc to CITATIONS.md**
-
-Add pmultiqc citation after the MultiQC entry.
-
-- [ ] **Step 5: Update README.md**
-
-Add DIA-NN version support table and link to `docs/parameters.md`.
-
-- [ ] **Step 6: Validate and commit**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-git add docs/usage.md docs/output.md CITATIONS.md README.md
-git commit -m "docs: complete usage.md, output.md, citations, README (#1, #3, #9, #15)
-
-- DDA mode documentation with limitations
-- Missing param sections (preprocessing, QC, extra_args scope)
-- Container version override and Singularity guides
-- Parquet vs TSV output explanation
-- pmultiqc citation added
-- README updated with version table
-
-Closes #3, #9, #15"
-```
-
----
-
-## Task 12: Close resolved issues
-
-- [ ] **Step 1: Close issues via GitHub CLI**
-
-```bash
-gh issue close 17 --repo bigbio/quantmsdiann --comment "Already implemented — --monitor-mod is extracted from diann_config.cfg (generated by sdrf-pipelines convert-diann) and passed to all DIA-NN steps via mod_flags."
-gh issue close 2 --repo bigbio/quantmsdiann --comment "Superseded by #4 (Phase 6: consolidate param generation to sdrf-pipelines)."
-gh issue close 1 --repo bigbio/quantmsdiann --comment "Resolved — docs/parameters.md created with comprehensive parameter reference."
-gh issue close 3 --repo bigbio/quantmsdiann --comment "Resolved — diann_extra_args scope documented in docs/usage.md."
-gh issue close 9 --repo bigbio/quantmsdiann --comment "Resolved — container version override guide and Singularity usage added to docs/usage.md."
-gh issue close 15 --repo bigbio/quantmsdiann --comment "Resolved — docs/usage.md input documentation updated."
-```
-
----
-
-## Task 13: Final validation and push
-
-- [ ] **Step 1: Run full validation suite**
-
-```bash
-conda run -n nfcore pre-commit run --all-files
-conda run -n nfcore nf-core pipelines lint --release --dir .
-```
-
-Expected: 0 failures on both.
-
-- [ ] **Step 2: Push dda branch and create PR**
-
-```bash
-git push -u origin dda
-gh pr create --title "feat: v1.0.0 release — robustness, DDA support, features, docs" --body "$(cat <<'PREOF'
-## Summary
-- Robustness fixes: pipefail, error_retry, empty input guards
-- DDA support via --diann_dda flag (DIA-NN >= 2.3.2)
-- New params: --light-models, --export-quant, --site-ms1-quant
-- InfinDIA groundwork (experimental)
-- DIA-NN 2.3.2 version config
-- New test configs: test_dda, test_dia_skip_preanalysis
-- Comprehensive docs: parameters.md, complete usage.md, output.md
-
-## Issues
-Closes #1, #3, #5, #7, #9, #10, #15, #17
-
-## Test plan
-- [ ] Existing CI tests pass (test_dia, test_dia_dotd)
-- [ ] New test_dda passes with BSA dataset on DIA-NN 2.3.2
-- [ ] test_dia_skip_preanalysis passes
-- [ ] nf-core lint --release: 0 failures
-- [ ] pre-commit: all passing
-PREOF
-)" --base dev
-```
diff --git a/lib/VersionUtils.groovy b/lib/VersionUtils.groovy
new file mode 100644
index 0000000..f340a61
--- /dev/null
+++ b/lib/VersionUtils.groovy
@@ -0,0 +1,34 @@
+/**
+ * Semantic version comparison utility for DIA-NN version guards.
+ *
+ * Nextflow auto-loads all classes in lib/, so these are available
+ * in workflows and module scripts without explicit imports.
+ */
+class VersionUtils {
+
+    /**
+     * Compare two version strings semantically (e.g. '2.10.0' > '2.3.2').
+     * Returns negative if a < b, zero if equal, positive if a > b.
+     */
+    static int compare(String a, String b) {
+        def partsA = a.tokenize('.').collect { it.isInteger() ? it.toInteger() : 0 }
+        def partsB = b.tokenize('.').collect { it.isInteger() ? it.toInteger() : 0 }
+        def maxLen = Math.max(partsA.size(), partsB.size())
+        for (int i = 0; i < maxLen; i++) {
+            int va = i < partsA.size() ? partsA[i] : 0
+            int vb = i < partsB.size() ? partsB[i] : 0
+            if (va != vb) return va <=> vb
+        }
+        return 0
+    }
+
+    /** True if version is strictly less than required. */
+    static boolean versionLessThan(String version, String required) {
+        return compare(version, required) < 0
+    }
+
+    /** True if version is greater than or equal to required. */
+    static boolean versionAtLeast(String version, String required) {
+        return compare(version, required) >= 0
+    }
+}
diff --git a/modules/local/diann/final_quantification/main.nf b/modules/local/diann/final_quantification/main.nf
index a16f551..00e5659 100644
--- a/modules/local/diann/final_quantification/main.nf
+++ b/modules/local/diann/final_quantification/main.nf
@@ -66,7 +66,7 @@ process FINAL_QUANTIFICATION {
     report_decoys = params.diann_report_decoys ? "--report-decoys": ""
     diann_export_xic = params.diann_export_xic ? "--xic": ""
     // --direct-quant only exists in DIA-NN >= 1.9.2 (QuantUMS counterpart); skip for older versions
-    quantums = params.quantums ? "" : (params.diann_version >= '1.9' ? "--direct-quant" : "")
+    quantums = params.quantums ? "" : (VersionUtils.versionAtLeast(params.diann_version, '1.9') ? "--direct-quant" : "")
     quantums_train_runs = params.quantums_train_runs ? "--quant-train-runs $params.quantums_train_runs": ""
     quantums_sel_runs = params.quantums_sel_runs ? "--quant-sel-runs $params.quantums_sel_runs": ""
     quantums_params = params.quantums_params ? "--quant-params $params.quantums_params": ""
diff --git a/modules/local/diann/individual_analysis/main.nf b/modules/local/diann/individual_analysis/main.nf
index b4e8507..a17af6a 100644
--- a/modules/local/diann/individual_analysis/main.nf
+++ b/modules/local/diann/individual_analysis/main.nf
@@ -86,8 +86,8 @@ process INDIVIDUAL_ANALYSIS {
     diann_dda_flag = params.diann_dda ? "--dda" : ""
 
     // Flags removed in DIA-NN 2.3.x — only pass for older versions
-    no_ifs_removal = params.diann_version < '2.3' ? "--no-ifs-removal" : ""
-    no_main_report = params.diann_version < '2.3' ? "--no-main-report" : ""
+    no_ifs_removal = VersionUtils.versionLessThan(params.diann_version, '2.3') ? "--no-ifs-removal" : ""
+    no_main_report = VersionUtils.versionLessThan(params.diann_version, '2.3') ? "--no-main-report" : ""
 
     // Per-file scan ranges from SDRF (empty = no flag, DIA-NN auto-detects)
     min_pr_mz = meta['ms1minmz'] ? "--min-pr-mz ${meta['ms1minmz']}" : ""
diff --git a/workflows/dia.nf b/workflows/dia.nf
index 351f4f2..be3f850 100644
--- a/workflows/dia.nf
+++ b/workflows/dia.nf
@@ -36,17 +36,17 @@ workflow DIA {
     ch_software_versions = channel.empty()
 
     // Version guard for DDA mode
-    if (params.diann_dda && params.diann_version < '2.3.2') {
+    if (params.diann_dda && VersionUtils.versionLessThan(params.diann_version, '2.3.2')) {
         error("DDA mode (--diann_dda) requires DIA-NN >= 2.3.2. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
     }
 
     // Version guard for InfinDIA
-    if (params.enable_infin_dia && params.diann_version < '2.3.0') {
+    if (params.enable_infin_dia && VersionUtils.versionLessThan(params.diann_version, '2.3.0')) {
         error("InfinDIA requires DIA-NN >= 2.3.0. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
     }
 
     // Version guard for DIA-NN 2.0+ features
-    if ((params.diann_light_models || params.diann_export_quant || params.diann_site_ms1_quant) && params.diann_version < '2.0') {
+    if ((params.diann_light_models || params.diann_export_quant || params.diann_site_ms1_quant) && VersionUtils.versionLessThan(params.diann_version, '2.0')) {
         def enabled = []
         if (params.diann_light_models) enabled << '--light-models'
         if (params.diann_export_quant) enabled << '--export-quant'

From 7df29e2663ae58b2730a31bc69d187edacce1468 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Tue, 7 Apr 2026 09:22:37 +0100
Subject: [PATCH 23/28] chore: bump version to 2.0.0dev for DDA support release

DDA analysis support is a major feature warranting a major version bump.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 8d8677c..dd305a0 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -373,7 +373,7 @@ manifest {
     mainScript      = 'main.nf'
     defaultBranch   = 'main'
     nextflowVersion = '!>=25.04.0'
-    version         = '1.0.1dev'
+    version         = '2.0.0dev'
     doi             = '10.5281/zenodo.15573386'
 }
 

From a3f4e2563f9c10f649cc298035d01f6d2735b2f2 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Tue, 7 Apr 2026 10:02:20 +0100
Subject: [PATCH 24/28] fix: standardize meta.yml naming, fix descriptions and
 minor issues
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Rename output version→versions in sdrf_parsing/meta.yml
- Add ch_ prefix to input_file→ch_input_file in input_check/meta.yml
- Fix grammar in pmultiqc and diann_msstats meta.yml descriptions
- Fix glob pattern in decompress_dotd/meta.yml (double-dot expansion)
- Update CITATIONS.md to link published Nature Methods article
- Fix schema_input.json error messages (source name, whitespace)
- Standardize quantmsdiann keyword in utils meta.yml

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 CITATIONS.md                                              | 2 +-
 assets/schema_input.json                                  | 4 ++--
 modules/local/diann/diann_msstats/meta.yml                | 2 +-
 modules/local/pmultiqc/meta.yml                           | 2 +-
 modules/local/sdrf_parsing/meta.yml                       | 2 +-
 modules/local/utils/decompress_dotd/meta.yml              | 2 +-
 subworkflows/local/input_check/meta.yml                   | 2 +-
 subworkflows/local/utils_nfcore_quantms_pipeline/meta.yml | 2 +-
 8 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/CITATIONS.md b/CITATIONS.md
index d74e0f9..8985a13 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -1,6 +1,6 @@
 # bigbio/quantmsdiann: Citations
 
-## [Pipeline](https://www.researchsquare.com/article/rs-3002027/v1)
+## [Pipeline](https://doi.org/10.1038/s41592-024-02343-1)
 
 > Dai C, Pfeuffer J, Wang H, Zheng P, Käll L, Sachsenberg T, Demichev V, Bai M, Kohlbacher O, Perez-Riverol Y. quantms: a cloud-based pipeline for quantitative proteomics enables the reanalysis of public proteomics data. Nat Methods. 2024 Jul 4. doi: 10.1038/s41592-024-02343-1. Epub ahead of print. PMID: 38965444.
 
diff --git a/assets/schema_input.json b/assets/schema_input.json
index 7b15010..1699aad 100644
--- a/assets/schema_input.json
+++ b/assets/schema_input.json
@@ -11,7 +11,7 @@
             "source name": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Source name must be provided and cannot contain spaces"
             },
             "comment[data file]": {
                 "type": "string",
@@ -22,7 +22,7 @@
             "assay name": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Assay name must be provided and cannot contain spaces",
+                "errorMessage": "Assay name must be provided and cannot contain whitespace",
                 "meta": ["assay"]
             }
         }
diff --git a/modules/local/diann/diann_msstats/meta.yml b/modules/local/diann/diann_msstats/meta.yml
index ac1f147..a440d61 100644
--- a/modules/local/diann/diann_msstats/meta.yml
+++ b/modules/local/diann/diann_msstats/meta.yml
@@ -17,7 +17,7 @@ input:
       pattern: "*.tsv"
   - exp_design:
       type: file
-      description: An experimental design file including Sample and replicates column et al.
+      description: An experimental design file including Sample and replicates column etc.
       pattern: "*.tsv"
   - report_pr:
       type: file
diff --git a/modules/local/pmultiqc/meta.yml b/modules/local/pmultiqc/meta.yml
index adf63f2..fcca33e 100644
--- a/modules/local/pmultiqc/meta.yml
+++ b/modules/local/pmultiqc/meta.yml
@@ -23,7 +23,7 @@ output:
       pattern: "*.html"
   - quantmsdb:
       type: file
-      description: Sqlite3 database file stored protein psm and quantification information
+      description: SQLite3 database file that stores protein, PSM, and quantification information
       pattern: "*.db"
   - data:
       type: dir
diff --git a/modules/local/sdrf_parsing/meta.yml b/modules/local/sdrf_parsing/meta.yml
index 7c311f4..846cfaa 100644
--- a/modules/local/sdrf_parsing/meta.yml
+++ b/modules/local/sdrf_parsing/meta.yml
@@ -28,7 +28,7 @@ output:
       type: file
       description: log file
       pattern: "*.log"
-  - version:
+  - versions:
       type: file
       description: File containing software version
       pattern: "versions.yml"
diff --git a/modules/local/utils/decompress_dotd/meta.yml b/modules/local/utils/decompress_dotd/meta.yml
index bbc7c58..55330d3 100644
--- a/modules/local/utils/decompress_dotd/meta.yml
+++ b/modules/local/utils/decompress_dotd/meta.yml
@@ -22,7 +22,7 @@ input:
       type: file
       description: |
         Bruker Raw file archived using tar
-      pattern: "*.{d.tar,.tar,.gz,.d.tar.gz}"
+      pattern: "*.{d.tar,tar,gz,d.tar.gz}"
 output:
   - meta:
       type: map
diff --git a/subworkflows/local/input_check/meta.yml b/subworkflows/local/input_check/meta.yml
index abe2c7f..3c88724 100644
--- a/subworkflows/local/input_check/meta.yml
+++ b/subworkflows/local/input_check/meta.yml
@@ -9,7 +9,7 @@ keywords:
 components:
   - samplesheet/check
 input:
-  - input_file:
+  - ch_input_file:
       type: file
       description: |
         Input file to be validated
diff --git a/subworkflows/local/utils_nfcore_quantms_pipeline/meta.yml b/subworkflows/local/utils_nfcore_quantms_pipeline/meta.yml
index 06365ae..cf1fd6d 100644
--- a/subworkflows/local/utils_nfcore_quantms_pipeline/meta.yml
+++ b/subworkflows/local/utils_nfcore_quantms_pipeline/meta.yml
@@ -4,7 +4,7 @@ description: Pipeline completion utilities for the nf-core quantmsdiann pipeline
 keywords:
   - utils
   - nf-core
-  - quantms
+  - quantmsdiann
 components:
   - completionemail
   - completionsummary

From fc96eeb95e608f797e4bb904bd42b59616412f58 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Tue, 7 Apr 2026 13:10:10 +0100
Subject: [PATCH 25/28] feat: auto-detect DDA mode from SDRF acquisition method
 column

DDA mode is now automatically detected from the SDRF
`comment[proteomics data acquisition method]` column when it contains
`data-dependent acquisition`. The `--diann_dda` flag is kept as a
fallback for SDRFs that lack this column.

- Modules now read acquisition method from meta instead of params
- INSILICO_LIBRARY_GENERATION receives is_dda as input from workflow
- Version guard triggers for both param and SDRF-detected DDA
- Updated docs, parameters, and schema to reflect auto-detection

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 docs/parameters.md                            | 33 ++++++++++---------
 docs/usage.md                                 | 13 ++++++--
 .../diann/assemble_empirical_library/main.nf  |  2 +-
 .../local/diann/final_quantification/main.nf  |  2 +-
 .../local/diann/individual_analysis/main.nf   |  2 +-
 .../diann/insilico_library_generation/main.nf |  3 +-
 .../insilico_library_generation/meta.yml      |  3 ++
 .../local/diann/preliminary_analysis/main.nf  |  2 +-
 nextflow.config                               |  2 +-
 nextflow_schema.json                          |  2 +-
 .../local/create_input_channel/main.nf        |  6 ++--
 workflows/dia.nf                              | 13 ++++++--
 12 files changed, 53 insertions(+), 30 deletions(-)

diff --git a/docs/parameters.md b/docs/parameters.md
index 0a3eac8..f3c76c0 100644
--- a/docs/parameters.md
+++ b/docs/parameters.md
@@ -52,16 +52,16 @@ This document lists every pipeline parameter organised by category. Default valu
 
 ## 5. DIA-NN General
 
-| Parameter                | Type    | Default | Description                                                                                                                                                                                                  |
-| ------------------------ | ------- | ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
-| `--diann_version`        | string  | `1.8.1` | DIA-NN version used by the workflow. Controls version-dependent flags (e.g. `--monitor-mod` for 1.8.x). See [DIA-NN Version Selection](usage.md#dia-nn-version-selection).                                   |
-| `--diann_debug`          | integer | `3`     | DIA-NN debug/verbosity level (0-4). Higher values produce more verbose logs.                                                                                                                                 |
-| `--diann_speclib`        | string  | `null`  | Path to an external spectral library. If provided, the in-silico library generation step is skipped.                                                                                                         |
-| `--diann_extra_args`     | string  | `null`  | Extra arguments appended to all DIA-NN steps. Flags incompatible with a step are automatically stripped with a warning. See [Passing Extra Arguments to DIA-NN](usage.md#passing-extra-arguments-to-dia-nn). |
-| `--diann_dda`            | boolean | `false` | Enable DDA (Data-Dependent Acquisition) analysis mode. Passes `--dda` to all DIA-NN steps. Requires DIA-NN >= 2.3.2. Beta feature.                                                                           |
-| `--diann_light_models`   | boolean | `false` | Enable `--light-models` for 10x faster in-silico library generation. Requires DIA-NN >= 2.0.                                                                                                                 |
-| `--diann_export_quant`   | boolean | `false` | Enable `--export-quant` for fragment-level parquet data export. Requires DIA-NN >= 2.0.                                                                                                                      |
-| `--diann_site_ms1_quant` | boolean | `false` | Enable `--site-ms1-quant` to use MS1 apex intensities for PTM site quantification. Requires DIA-NN >= 2.0.                                                                                                   |
+| Parameter                | Type    | Default | Description                                                                                                                                                                                                     |
+| ------------------------ | ------- | ------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
+| `--diann_version`        | string  | `1.8.1` | DIA-NN version used by the workflow. Controls version-dependent flags (e.g. `--monitor-mod` for 1.8.x). See [DIA-NN Version Selection](usage.md#dia-nn-version-selection).                                      |
+| `--diann_debug`          | integer | `3`     | DIA-NN debug/verbosity level (0-4). Higher values produce more verbose logs.                                                                                                                                    |
+| `--diann_speclib`        | string  | `null`  | Path to an external spectral library. If provided, the in-silico library generation step is skipped.                                                                                                            |
+| `--diann_extra_args`     | string  | `null`  | Extra arguments appended to all DIA-NN steps. Flags incompatible with a step are automatically stripped with a warning. See [Passing Extra Arguments to DIA-NN](usage.md#passing-extra-arguments-to-dia-nn).    |
+| `--diann_dda`            | boolean | `false` | Explicitly enable DDA mode. Normally auto-detected from the SDRF `comment[proteomics data acquisition method]` column. Use this flag only when the SDRF lacks the acquisition method. Requires DIA-NN >= 2.3.2. |
+| `--diann_light_models`   | boolean | `false` | Enable `--light-models` for 10x faster in-silico library generation. Requires DIA-NN >= 2.0.                                                                                                                    |
+| `--diann_export_quant`   | boolean | `false` | Enable `--export-quant` for fragment-level parquet data export. Requires DIA-NN >= 2.0.                                                                                                                         |
+| `--diann_site_ms1_quant` | boolean | `false` | Enable `--site-ms1-quant` to use MS1 apex intensities for PTM site quantification. Requires DIA-NN >= 2.0.                                                                                                      |
 
 ## 6. Mass Accuracy & Calibration
 
@@ -123,13 +123,14 @@ This document lists every pipeline parameter organised by category. Default valu
 
 ## 12. DDA Mode
 
-| Parameter     | Type    | Default | Description                                                                                                                                                                                                   |
-| ------------- | ------- | ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| `--diann_dda` | boolean | `false` | Enable DDA analysis mode. Passes `--dda` to all DIA-NN steps. Requires DIA-NN >= 2.3.2 (use `-profile diann_v2_3_2`). This is a beta feature with known limitations; see the usage documentation for details. |
+| Parameter     | Type    | Default | Description                                                                                                                                                                                                                                |
+| ------------- | ------- | ------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ |
+| `--diann_dda` | boolean | `false` | Explicitly enable DDA mode when SDRF lacks the acquisition method column. Normally DDA is auto-detected from the SDRF `comment[proteomics data acquisition method]`. Requires DIA-NN >= 2.3.2 (use `-profile diann_v2_3_2`). Beta feature. |
 
-> **Note:** DDA support requires DIA-NN >= 2.3.2. Enable this profile with
-> `-profile diann_v2_3_2`. The DDA mode is experimental and may not support
-> all pipeline features available in DIA mode.
+> **Note:** DDA mode is auto-detected from the SDRF when the `comment[proteomics data acquisition method]`
+> column contains `data-dependent acquisition`. The `--diann_dda` flag is only needed as a
+> fallback when the SDRF does not include this column. DDA requires DIA-NN >= 2.3.2
+> (`-profile diann_v2_3_2`).
 
 ## 13. InfinDIA (Experimental)
 
diff --git a/docs/usage.md b/docs/usage.md
index 4055f47..8b696df 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -66,7 +66,16 @@ For Synchro-PASEF data, enable `--diann_tims_sum` (which adds `--quant-tims-sum`
 
 ### DDA Analysis Mode (Beta)
 
-DIA-NN 2.3.2+ supports DDA data analysis via the `--dda` flag. Enable it with:
+DIA-NN 2.3.2+ supports DDA data analysis via the `--dda` flag. The pipeline **auto-detects DDA mode** from the SDRF `comment[proteomics data acquisition method]` column — no extra flags needed if your SDRF contains `data-dependent acquisition`:
+
+```bash
+nextflow run bigbio/quantmsdiann \
+  --input dda_sdrf.tsv \
+  --database proteins.fasta \
+  -profile diann_v2_3_2,docker
+```
+
+If your SDRF does not include the acquisition method column, you can explicitly enable DDA mode with `--diann_dda true`:
 
 ```bash
 nextflow run bigbio/quantmsdiann \
@@ -84,7 +93,7 @@ nextflow run bigbio/quantmsdiann \
 - No isobaric labeling or reporter-tag quantification
 - Primary use cases: legacy DDA reanalysis, spectral library creation, immunopeptidomics
 
-The pipeline uses the same workflow for DDA as DIA — the `--dda` flag is passed to all DIA-NN steps automatically.
+The pipeline uses the same workflow for DDA as DIA — the `--dda` flag is passed to all DIA-NN steps automatically when DDA is detected from the SDRF or enabled via `--diann_dda`.
 
 ### Preprocessing Options
 
diff --git a/modules/local/diann/assemble_empirical_library/main.nf b/modules/local/diann/assemble_empirical_library/main.nf
index b3f0181..2bfb67e 100644
--- a/modules/local/diann/assemble_empirical_library/main.nf
+++ b/modules/local/diann/assemble_empirical_library/main.nf
@@ -54,7 +54,7 @@ process ASSEMBLE_EMPIRICAL_LIBRARY {
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
     diann_tims_sum = params.diann_tims_sum ? "--quant-tims-sum" : ""
     diann_im_window = params.diann_im_window ? "--im-window $params.diann_im_window" : ""
-    diann_dda_flag = params.diann_dda ? "--dda" : ""
+    diann_dda_flag = meta.acquisition_method == 'dda' ? "--dda" : ""
 
     """
     # Precursor Tolerance value was: ${meta['precursormasstolerance']}
diff --git a/modules/local/diann/final_quantification/main.nf b/modules/local/diann/final_quantification/main.nf
index 00e5659..a1ba609 100644
--- a/modules/local/diann/final_quantification/main.nf
+++ b/modules/local/diann/final_quantification/main.nf
@@ -72,7 +72,7 @@ process FINAL_QUANTIFICATION {
     quantums_params = params.quantums_params ? "--quant-params $params.quantums_params": ""
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
     diann_use_quant = params.diann_use_quant ? "--use-quant" : ""
-    diann_dda_flag = params.diann_dda ? "--dda" : ""
+    diann_dda_flag = meta.acquisition_method == 'dda' ? "--dda" : ""
     diann_export_quant = params.diann_export_quant ? "--export-quant" : ""
     diann_site_ms1_quant = params.diann_site_ms1_quant ? "--site-ms1-quant" : ""
 
diff --git a/modules/local/diann/individual_analysis/main.nf b/modules/local/diann/individual_analysis/main.nf
index a17af6a..975ceaf 100644
--- a/modules/local/diann/individual_analysis/main.nf
+++ b/modules/local/diann/individual_analysis/main.nf
@@ -83,7 +83,7 @@ process INDIVIDUAL_ANALYSIS {
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
     diann_tims_sum = params.diann_tims_sum ? "--quant-tims-sum" : ""
     diann_im_window = params.diann_im_window ? "--im-window $params.diann_im_window" : ""
-    diann_dda_flag = params.diann_dda ? "--dda" : ""
+    diann_dda_flag = meta.acquisition_method == 'dda' ? "--dda" : ""
 
     // Flags removed in DIA-NN 2.3.x — only pass for older versions
     no_ifs_removal = VersionUtils.versionLessThan(params.diann_version, '2.3') ? "--no-ifs-removal" : ""
diff --git a/modules/local/diann/insilico_library_generation/main.nf b/modules/local/diann/insilico_library_generation/main.nf
index 7de4665..8b05859 100644
--- a/modules/local/diann/insilico_library_generation/main.nf
+++ b/modules/local/diann/insilico_library_generation/main.nf
@@ -11,6 +11,7 @@ process INSILICO_LIBRARY_GENERATION {
     input:
     path(fasta)
     path(diann_config)
+    val(is_dda)
 
     output:
     path "versions.yml", emit: versions
@@ -47,7 +48,7 @@ process INSILICO_LIBRARY_GENERATION {
     max_fr_mz = params.max_fr_mz ? "--max-fr-mz $params.max_fr_mz":""
     met_excision = params.met_excision ? "--met-excision" : ""
     diann_no_peptidoforms = params.diann_no_peptidoforms ? "--no-peptidoforms" : ""
-    diann_dda_flag = params.diann_dda ? "--dda" : ""
+    diann_dda_flag = is_dda ? "--dda" : ""
     diann_light_models = params.diann_light_models ? "--light-models" : ""
     infin_dia_flag = params.enable_infin_dia ? "--infin-dia" : ""
     pre_select_flag = params.diann_pre_select ? "--pre-select $params.diann_pre_select" : ""
diff --git a/modules/local/diann/insilico_library_generation/meta.yml b/modules/local/diann/insilico_library_generation/meta.yml
index 5f9d68b..a6185d7 100644
--- a/modules/local/diann/insilico_library_generation/meta.yml
+++ b/modules/local/diann/insilico_library_generation/meta.yml
@@ -19,6 +19,9 @@ input:
       type: file
       description: specifies a configuration file to load options/commands from.
       pattern: "*.cfg"
+  - is_dda:
+      type: boolean
+      description: Whether DDA mode is enabled (auto-detected from SDRF or set via --diann_dda)
 output:
   - predict_speclib:
       type: file
diff --git a/modules/local/diann/preliminary_analysis/main.nf b/modules/local/diann/preliminary_analysis/main.nf
index 7e24280..f9a3508 100644
--- a/modules/local/diann/preliminary_analysis/main.nf
+++ b/modules/local/diann/preliminary_analysis/main.nf
@@ -68,7 +68,7 @@ process PRELIMINARY_ANALYSIS {
     scan_window = params.scan_window_automatic ? '' : "--window $params.scan_window"
     diann_tims_sum = params.diann_tims_sum ? "--quant-tims-sum" : ""
     diann_im_window = params.diann_im_window ? "--im-window $params.diann_im_window" : ""
-    diann_dda_flag = params.diann_dda ? "--dda" : ""
+    diann_dda_flag = meta.acquisition_method == 'dda' ? "--dda" : ""
 
     // Per-file scan ranges from SDRF (empty = no flag, DIA-NN auto-detects)
     min_pr_mz = meta['ms1minmz'] ? "--min-pr-mz ${meta['ms1minmz']}" : ""
diff --git a/nextflow.config b/nextflow.config
index dd305a0..696ebc4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -52,7 +52,7 @@ params {
     diann_debug             = 3
     diann_speclib           = null
     diann_extra_args        = null
-    diann_dda               = false  // Enable DDA analysis mode (requires DIA-NN >= 2.3.2)
+    diann_dda               = false  // Fallback: explicitly enable DDA when SDRF lacks acquisition method (requires DIA-NN >= 2.3.2)
     diann_light_models      = false  // add '--light-models' for 10x faster library generation (DIA-NN >= 2.0)
     diann_export_quant      = false  // add '--export-quant' for fragment-level parquet export (DIA-NN >= 2.0)
     diann_site_ms1_quant    = false  // add '--site-ms1-quant' for MS1 apex PTM quantification (DIA-NN >= 2.0)
diff --git a/nextflow_schema.json b/nextflow_schema.json
index ebe3a45..08d564b 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -458,7 +458,7 @@
                 },
                 "diann_dda": {
                     "type": "boolean",
-                    "description": "Enable DDA (Data-Dependent Acquisition) analysis mode. Passes --dda to all DIA-NN steps. Requires DIA-NN >= 2.3.2 (use -profile diann_v2_3_2). Beta feature.",
+                    "description": "Explicitly enable DDA mode. Normally auto-detected from the SDRF acquisition method column. Use only when SDRF lacks this column. Requires DIA-NN >= 2.3.2.",
                     "fa_icon": "fas fa-flask",
                     "default": false
                 },
diff --git a/subworkflows/local/create_input_channel/main.nf b/subworkflows/local/create_input_channel/main.nf
index c0249f1..a52b9ee 100644
--- a/subworkflows/local/create_input_channel/main.nf
+++ b/subworkflows/local/create_input_channel/main.nf
@@ -72,16 +72,16 @@ def create_meta_channel(LinkedHashMap row, enzymes, files, wrapper) {
         exit(1, "ERROR: Please check input file -> File Uri does not exist!\n${filestr}")
     }
 
-    // Validate acquisition method
+    // Detect acquisition method from SDRF or fallback to --diann_dda param
     def acqMethod = row.AcquisitionMethod?.toString()?.trim() ?: ""
     if (acqMethod.toLowerCase().contains("data-independent acquisition") || acqMethod.toLowerCase().contains("dia")) {
         meta.acquisition_method = "dia"
-    } else if (params.diann_dda && (acqMethod.toLowerCase().contains("data-dependent acquisition") || acqMethod.toLowerCase().contains("dda"))) {
+    } else if (acqMethod.toLowerCase().contains("data-dependent acquisition") || acqMethod.toLowerCase().contains("dda")) {
         meta.acquisition_method = "dda"
     } else if (acqMethod.isEmpty()) {
         meta.acquisition_method = params.diann_dda ? "dda" : "dia"
     } else {
-        log.error("Unsupported acquisition method: '${acqMethod}'. This pipeline supports DIA" + (params.diann_dda ? " and DDA (--diann_dda)" : "") + ". Found in file: ${filestr}")
+        log.error("Unsupported acquisition method: '${acqMethod}'. This pipeline supports DIA and DDA. Found in file: ${filestr}")
         exit(1)
     }
 
diff --git a/workflows/dia.nf b/workflows/dia.nf
index be3f850..69dd78d 100644
--- a/workflows/dia.nf
+++ b/workflows/dia.nf
@@ -35,7 +35,7 @@ workflow DIA {
 
     ch_software_versions = channel.empty()
 
-    // Version guard for DDA mode
+    // Version guard for DDA mode (when explicitly set via param)
     if (params.diann_dda && VersionUtils.versionLessThan(params.diann_version, '2.3.2')) {
         error("DDA mode (--diann_dda) requires DIA-NN >= 2.3.2. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
     }
@@ -68,6 +68,15 @@ workflow DIA {
         .ifEmpty { error("No valid input files found after SDRF parsing. Check your SDRF file and input paths.") }
         .first()
 
+    // Determine DDA mode: true if explicitly set via param OR auto-detected from SDRF
+    ch_is_dda = ch_experiment_meta.map { meta ->
+        def dda = params.diann_dda || meta.acquisition_method == 'dda'
+        if (dda && VersionUtils.versionLessThan(params.diann_version, '2.3.2')) {
+            error("DDA mode (detected from SDRF) requires DIA-NN >= 2.3.2. Current version: ${params.diann_version}. Use -profile diann_v2_3_2")
+        }
+        return dda
+    }
+
     // diann_config.cfg comes directly from SDRF_PARSING (convert-diann)
     // Use as value channel so it can be consumed by all per-file processes
     ch_diann_cfg_val = ch_diann_cfg
@@ -78,7 +87,7 @@ workflow DIA {
     if (params.diann_speclib != null && params.diann_speclib.toString() != "") {
         speclib = channel.from(file(params.diann_speclib, checkIfExists: true))
     } else {
-        INSILICO_LIBRARY_GENERATION(ch_searchdb, ch_diann_cfg_val)
+        INSILICO_LIBRARY_GENERATION(ch_searchdb, ch_diann_cfg_val, ch_is_dda)
         speclib = INSILICO_LIBRARY_GENERATION.out.predict_speclib
     }
 

From 9f4ee58d98a90a9eaec8ec03381519da7748f709 Mon Sep 17 00:00:00 2001
From: Yasset Perez-Riverol <ypriverol@gmail.com>
Date: Tue, 7 Apr 2026 13:14:07 +0100
Subject: [PATCH 26/28] fix: address Copilot review comments

- Revert meta.yml input_file naming to match workflow interface
- Gate --pre-select behind enable_infin_dia (InfinDIA-only flag)
- Tighten --direct-quant version check from 1.9 to 1.9.2
- Improve GHCR login: guard both token and username, skip test_dda
  gracefully on fork PRs where credentials are unavailable

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
---
 .github/workflows/ci.yml                               | 10 +++++++---
 modules/local/diann/final_quantification/main.nf       |  4 ++--
 .../local/diann/insilico_library_generation/main.nf    |  2 +-
 subworkflows/local/input_check/meta.yml                |  4 ++--
 4 files changed, 12 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index aadf1dd..e80a477 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -64,16 +64,20 @@ jobs:
         if: matrix.test_profile == 'test_dda'
         env:
           GHCR_TOKEN: ${{ secrets.GHCR_TOKEN }}
+          GHCR_USERNAME: ${{ secrets.GHCR_USERNAME }}
         run: |
-          if [ -n "$GHCR_TOKEN" ]; then
-            echo "${{ secrets.GHCR_TOKEN }}" | docker login ghcr.io -u ${{ secrets.GHCR_USERNAME }} --password-stdin
+          if [ -z "$GHCR_TOKEN" ] || [ -z "$GHCR_USERNAME" ]; then
+            echo "::warning::Skipping test_dda: GHCR credentials not available (expected for fork PRs)"
+            echo "SKIP_DDA=true" >> $GITHUB_ENV
+            exit 0
           fi
+          echo "$GHCR_TOKEN" | docker login ghcr.io -u "$GHCR_USERNAME" --password-stdin
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@v1.3.1
 
       - name: Run pipeline with test data in docker/singularity profile
-        if: github.event.pull_request.base.ref != 'master'
+        if: github.event.pull_request.base.ref != 'master' && env.SKIP_DDA != 'true'
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE,dev --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
 
diff --git a/modules/local/diann/final_quantification/main.nf b/modules/local/diann/final_quantification/main.nf
index a1ba609..64aa5cc 100644
--- a/modules/local/diann/final_quantification/main.nf
+++ b/modules/local/diann/final_quantification/main.nf
@@ -65,8 +65,8 @@ process FINAL_QUANTIFICATION {
     no_norm = params.diann_normalize ? "" : "--no-norm"
     report_decoys = params.diann_report_decoys ? "--report-decoys": ""
     diann_export_xic = params.diann_export_xic ? "--xic": ""
-    // --direct-quant only exists in DIA-NN >= 1.9.2 (QuantUMS counterpart); skip for older versions
-    quantums = params.quantums ? "" : (VersionUtils.versionAtLeast(params.diann_version, '1.9') ? "--direct-quant" : "")
+    // --direct-quant exists in DIA-NN >= 1.9.2 (QuantUMS counterpart); skip for older versions
+    quantums = params.quantums ? "" : (VersionUtils.versionAtLeast(params.diann_version, '1.9.2') ? "--direct-quant" : "")
     quantums_train_runs = params.quantums_train_runs ? "--quant-train-runs $params.quantums_train_runs": ""
     quantums_sel_runs = params.quantums_sel_runs ? "--quant-sel-runs $params.quantums_sel_runs": ""
     quantums_params = params.quantums_params ? "--quant-params $params.quantums_params": ""
diff --git a/modules/local/diann/insilico_library_generation/main.nf b/modules/local/diann/insilico_library_generation/main.nf
index 8b05859..66bca5e 100644
--- a/modules/local/diann/insilico_library_generation/main.nf
+++ b/modules/local/diann/insilico_library_generation/main.nf
@@ -51,7 +51,7 @@ process INSILICO_LIBRARY_GENERATION {
     diann_dda_flag = is_dda ? "--dda" : ""
     diann_light_models = params.diann_light_models ? "--light-models" : ""
     infin_dia_flag = params.enable_infin_dia ? "--infin-dia" : ""
-    pre_select_flag = params.diann_pre_select ? "--pre-select $params.diann_pre_select" : ""
+    pre_select_flag = (params.enable_infin_dia && params.diann_pre_select) ? "--pre-select $params.diann_pre_select" : ""
 
     """
     diann `cat ${diann_config}` \\
diff --git a/subworkflows/local/input_check/meta.yml b/subworkflows/local/input_check/meta.yml
index 3c88724..1f2cefb 100644
--- a/subworkflows/local/input_check/meta.yml
+++ b/subworkflows/local/input_check/meta.yml
@@ -9,12 +9,12 @@ keywords:
 components:
   - samplesheet/check
 input:
-  - ch_input_file:
+  - input_file:
       type: file
       description: |
         Input file to be validated
 output:
-  - ch_input_file:
+  - input_file:
       type: file
       description: |
         Channel containing validated input files

From f04e754d0d17361686748c79369fa9e8ab5e2ddb Mon Sep 17 00:00:00 2001
From: yueqixuan <yueqx@foxmail.com>
Date: Wed, 8 Apr 2026 10:59:01 +0800
Subject: [PATCH 27/28] Support multiplexing

---
 .../local/diann/final_quantification/main.nf  |  14 +-
 nextflow.config                               |   2 +
 nextflow_schema.json                          |  13 ++
 .../local/create_input_channel/main.nf        | 136 ++++++++----------
 4 files changed, 86 insertions(+), 79 deletions(-)

diff --git a/modules/local/diann/final_quantification/main.nf b/modules/local/diann/final_quantification/main.nf
index 64aa5cc..f83af13 100644
--- a/modules/local/diann/final_quantification/main.nf
+++ b/modules/local/diann/final_quantification/main.nf
@@ -25,11 +25,11 @@ process FINAL_QUANTIFICATION {
     path "diann_report.{tsv,parquet}", emit: main_report, optional: true
     path "diann_report.manifest.txt", emit: report_manifest, optional: true
     path "diann_report.protein_description.tsv", emit: protein_description, optional: true
-    path "diann_report.stats.tsv", emit: report_stats
-    path "diann_report.pr_matrix.tsv", emit: pr_matrix
-    path "diann_report.pg_matrix.tsv", emit: pg_matrix
-    path "diann_report.gg_matrix.tsv", emit: gg_matrix
-    path "diann_report.unique_genes_matrix.tsv", emit: unique_gene_matrix
+    path "diann_report.stats.tsv", emit: report_stats, optional: true
+    path "diann_report.pr_matrix.tsv", emit: pr_matrix, optional: true
+    path "diann_report.pg_matrix.tsv", emit: pg_matrix, optional: true
+    path "diann_report.gg_matrix.tsv", emit: gg_matrix, optional: true
+    path "diann_report.unique_genes_matrix.tsv", emit: unique_gene_matrix, optional: true
     path "diannsummary.log", emit: log
 
     // Different library files format are exported due to different DIA-NN versions
@@ -75,6 +75,8 @@ process FINAL_QUANTIFICATION {
     diann_dda_flag = meta.acquisition_method == 'dda' ? "--dda" : ""
     diann_export_quant = params.diann_export_quant ? "--export-quant" : ""
     diann_site_ms1_quant = params.diann_site_ms1_quant ? "--site-ms1-quant" : ""
+    diann_channel_run_norm = params.diann_channel_run_norm ? "--channel-run-norm" : ""
+    diann_channel_spec_norm = params.diann_channel_spec_norm ? "--channel-spec-norm" : ""
 
     """
     # Notes: if .quant files are passed, mzml/.d files are not accessed, so the name needs to be passed but files
@@ -107,6 +109,8 @@ process FINAL_QUANTIFICATION {
             ${diann_dda_flag} \\
             ${diann_export_quant} \\
             ${diann_site_ms1_quant} \\
+            ${diann_channel_run_norm} \\
+            ${diann_channel_spec_norm} \\
             \${mod_flags} \\
             $args
 
diff --git a/nextflow.config b/nextflow.config
index 696ebc4..a8fbb0d 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -101,6 +101,8 @@ params {
     quantums_params         = null
     diann_no_peptidoforms   = false // add '--no-peptidoforms'
     diann_use_quant         = true // add '--use-quant' to FINAL_QUANTIFICATION
+    diann_channel_run_norm  = false // add '--channel-run-norm' to FINAL_QUANTIFICATION
+    diann_channel_spec_norm = false // add '--channel-spec-norm' to FINAL_QUANTIFICATION
 
     // pmultiqc options
     enable_pmultiqc          = true
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 08d564b..9fe8f21 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -411,6 +411,19 @@
                     "fa_icon": "far fa-check-square",
                     "default": true
                 },
+
+                "diann_channel_run_norm": {
+                    "type": "boolean",
+                    "description": "Set '--channel-run-norm'. Run-specific normalisation for multiplexing (e.g., Protein Turnover SILAC)",
+                    "fa_icon": "far fa-check-square",
+                    "default": false
+                },
+                "diann_channel_spec_norm": {
+                    "type": "boolean",
+                    "description": "Set '--channel-spec-norm'. Channel-specific normalisation for multiplexing (Independent Samples)",
+                    "fa_icon": "far fa-check-square",
+                    "default": false
+                },
                 "skip_preliminary_analysis": {
                     "type": "boolean",
                     "description": "Skip the preliminary analysis step, thus use the passed spectral library as-is instead of generating a local consensus library.",
diff --git a/subworkflows/local/create_input_channel/main.nf b/subworkflows/local/create_input_channel/main.nf
index a52b9ee..577441b 100644
--- a/subworkflows/local/create_input_channel/main.nf
+++ b/subworkflows/local/create_input_channel/main.nf
@@ -29,8 +29,23 @@ workflow CREATE_INPUT_CHANNEL {
         .combine(ch_expdesign)
         .splitCsv(header: true, sep: '\t')
         .map { experiment_id, row ->
+            def filestr
+            if (!params.root_folder) {
+                filestr = row.URI?.toString()?.trim() ? row.URI.toString() : row.Filename.toString()
+            } else {
+                filestr = row.Filename.toString()
+                filestr = params.root_folder + File.separator + filestr
+                filestr = (params.local_input_type
+                    ? filestr.take(filestr.lastIndexOf('.')) + '.' + params.local_input_type
+                    : filestr)
+            }
+            return [filestr, experiment_id, row]
+        }
+        .groupTuple(by: 0)
+        .map { filestr, experiment_ids, rows ->
+            def experiment_id = experiment_ids[0]
             def wrapper = [acquisition_method: "", experiment_id: experiment_id]
-            create_meta_channel(row, enzymes, files, wrapper)
+            return create_meta_channel_grouped(filestr, rows, wrapper)
         }
         .set { ch_meta_config_dia }
 
@@ -42,38 +57,23 @@ workflow CREATE_INPUT_CHANNEL {
 }
 
 // Function to get list of [meta, [ spectra_files ]]
-def create_meta_channel(LinkedHashMap row, enzymes, files, wrapper) {
+def create_meta_channel_grouped(String filestr, List rows, Map wrapper) {
     def meta = [:]
-    def filestr
 
-    // Always use SDRF format
-    if (!params.root_folder) {
-        filestr = row.URI?.toString()?.trim() ? row.URI.toString() : row.Filename.toString()
-    }
-    else {
-        filestr = row.Filename.toString()
-    }
+    def base_row = rows[0]
 
     def fileName = file(filestr).name
     def dotIndex = fileName.lastIndexOf('.')
     meta.id = dotIndex > 0 ? fileName.take(dotIndex) : fileName
     meta.experiment_id = wrapper.experiment_id
 
-    // apply transformations given by specified root_folder and type
-    if (params.root_folder) {
-        filestr = params.root_folder + File.separator + filestr
-        filestr = (params.local_input_type
-            ? filestr.take(filestr.lastIndexOf('.')) + '.' + params.local_input_type
-            : filestr)
-    }
-
     // existence check
     if (!file(filestr).exists()) {
         exit(1, "ERROR: Please check input file -> File Uri does not exist!\n${filestr}")
     }
 
     // Detect acquisition method from SDRF or fallback to --diann_dda param
-    def acqMethod = row.AcquisitionMethod?.toString()?.trim() ?: ""
+    def acqMethod = base_row.AcquisitionMethod?.toString()?.trim() ?: ""
     if (acqMethod.toLowerCase().contains("data-independent acquisition") || acqMethod.toLowerCase().contains("dia")) {
         meta.acquisition_method = "dia"
     } else if (acqMethod.toLowerCase().contains("data-dependent acquisition") || acqMethod.toLowerCase().contains("dda")) {
@@ -85,21 +85,35 @@ def create_meta_channel(LinkedHashMap row, enzymes, files, wrapper) {
         exit(1)
     }
 
-    // DissociationMethod is already normalized by convert-diann (HCD, CID, ETD, ECD)
-    meta.dissociationmethod = row.DissociationMethod?.toString()?.trim() ?: ""
-
+    meta.dissociationmethod = base_row.DissociationMethod?.toString()?.trim() ?: ""
     wrapper.acquisition_method = meta.acquisition_method
 
-    // Validate required SDRF columns - these parameters are exclusively read from SDRF (no command-line override)
+    def labels = rows.collect { it.Label?.toString()?.trim() }.findAll { it }.unique()
+    meta.labelling_type = labels.join(';')
+
+    def is_plexdia = labels.size() > 1 || (labels.size() == 1 && !labels[0].toLowerCase().contains("label free"))
+    meta.plexdia = is_plexdia
+
+    def enzymes = rows.collect { it.Enzyme?.toString()?.trim() }.findAll { it }.unique()
+    if (enzymes.size() > 1) {
+        log.error("Currently only one enzyme is supported per file. Found conflicting enzymes for ${filestr}: '${enzymes}'.")
+        exit(1)
+    }
+    meta.enzyme = enzymes ? enzymes[0] : null
+
+    def fixedMods = rows.collect { it.FixedModifications?.toString()?.trim() }.findAll { it }.unique()
+    meta.fixedmodifications = fixedMods ? fixedMods[0] : null
+
+    // Validate required SDRF columns 
     def requiredColumns = [
-        'Label': row.Label,
-        'Enzyme': row.Enzyme,
-        'FixedModifications': row.FixedModifications
+        'Label': meta.labelling_type,
+        'Enzyme': meta.enzyme,
+        'FixedModifications': meta.fixedmodifications
     ]
 
     def missingColumns = []
     requiredColumns.each { colName, colValue ->
-        if (colValue == null || colValue.toString().trim().isEmpty()) {
+        if (colValue == null || colValue.toString().isEmpty()) {
             missingColumns.add(colName)
         }
     }
@@ -110,20 +124,13 @@ def create_meta_channel(LinkedHashMap row, enzymes, files, wrapper) {
         exit(1)
     }
 
-    // Set values from SDRF (required columns)
-    meta.labelling_type = row.Label
-    meta.fixedmodifications = row.FixedModifications
-    meta.enzyme = row.Enzyme
-
-    // Set tolerance values: use SDRF if available, otherwise fall back to params
     def validUnits = ['ppm', 'da', 'Da', 'PPM']
 
-    // Precursor mass tolerance
-    if (row.PrecursorMassTolerance != null && !row.PrecursorMassTolerance.toString().trim().isEmpty()) {
+    if (base_row.PrecursorMassTolerance != null && !base_row.PrecursorMassTolerance.toString().trim().isEmpty()) {
         try {
-            meta.precursormasstolerance = Double.parseDouble(row.PrecursorMassTolerance)
+            meta.precursormasstolerance = Double.parseDouble(base_row.PrecursorMassTolerance)
         } catch (NumberFormatException e) {
-            log.error("ERROR: Invalid PrecursorMassTolerance value '${row.PrecursorMassTolerance}' for file '${filestr}'. Must be a valid number.")
+            log.error("ERROR: Invalid PrecursorMassTolerance value '${base_row.PrecursorMassTolerance}' for file '${filestr}'. Must be a valid number.")
             exit(1)
         }
     } else {
@@ -131,23 +138,21 @@ def create_meta_channel(LinkedHashMap row, enzymes, files, wrapper) {
         meta.precursormasstolerance = params.precursor_mass_tolerance
     }
 
-    // Precursor mass tolerance unit
-    if (row.PrecursorMassToleranceUnit != null && !row.PrecursorMassToleranceUnit.toString().trim().isEmpty()) {
-        if (!validUnits.any { row.PrecursorMassToleranceUnit.toString().equalsIgnoreCase(it) }) {
-            log.error("ERROR: Invalid PrecursorMassToleranceUnit '${row.PrecursorMassToleranceUnit}' for file '${filestr}'. Must be 'ppm' or 'Da'.")
+    if (base_row.PrecursorMassToleranceUnit != null && !base_row.PrecursorMassToleranceUnit.toString().trim().isEmpty()) {
+        if (!validUnits.any { base_row.PrecursorMassToleranceUnit.toString().equalsIgnoreCase(it) }) {
+            log.error("ERROR: Invalid PrecursorMassToleranceUnit '${base_row.PrecursorMassToleranceUnit}' for file '${filestr}'. Must be 'ppm' or 'Da'.")
             exit(1)
         }
-        meta.precursormasstoleranceunit = row.PrecursorMassToleranceUnit
+        meta.precursormasstoleranceunit = base_row.PrecursorMassToleranceUnit
     } else {
         meta.precursormasstoleranceunit = params.precursor_mass_tolerance_unit
     }
 
-    // Fragment mass tolerance
-    if (row.FragmentMassTolerance != null && !row.FragmentMassTolerance.toString().trim().isEmpty()) {
+    if (base_row.FragmentMassTolerance != null && !base_row.FragmentMassTolerance.toString().trim().isEmpty()) {
         try {
-            meta.fragmentmasstolerance = Double.parseDouble(row.FragmentMassTolerance)
+            meta.fragmentmasstolerance = Double.parseDouble(base_row.FragmentMassTolerance)
         } catch (NumberFormatException e) {
-            log.error("ERROR: Invalid FragmentMassTolerance value '${row.FragmentMassTolerance}' for file '${filestr}'. Must be a valid number.")
+            log.error("ERROR: Invalid FragmentMassTolerance value '${base_row.FragmentMassTolerance}' for file '${filestr}'. Must be a valid number.")
             exit(1)
         }
     } else {
@@ -155,43 +160,26 @@ def create_meta_channel(LinkedHashMap row, enzymes, files, wrapper) {
         meta.fragmentmasstolerance = params.fragment_mass_tolerance
     }
 
-    // Fragment mass tolerance unit
-    if (row.FragmentMassToleranceUnit != null && !row.FragmentMassToleranceUnit.toString().trim().isEmpty()) {
-        if (!validUnits.any { row.FragmentMassToleranceUnit.toString().equalsIgnoreCase(it) }) {
-            log.error("ERROR: Invalid FragmentMassToleranceUnit '${row.FragmentMassToleranceUnit}' for file '${filestr}'. Must be 'ppm' or 'Da'.")
+    if (base_row.FragmentMassToleranceUnit != null && !base_row.FragmentMassToleranceUnit.toString().trim().isEmpty()) {
+        if (!validUnits.any { base_row.FragmentMassToleranceUnit.toString().equalsIgnoreCase(it) }) {
+            log.error("ERROR: Invalid FragmentMassToleranceUnit '${base_row.FragmentMassToleranceUnit}' for file '${filestr}'. Must be 'ppm' or 'Da'.")
             exit(1)
         }
-        meta.fragmentmasstoleranceunit = row.FragmentMassToleranceUnit
+        meta.fragmentmasstoleranceunit = base_row.FragmentMassToleranceUnit
     } else {
         meta.fragmentmasstoleranceunit = params.fragment_mass_tolerance_unit
     }
 
-    // Variable modifications: use SDRF if available, otherwise fall back to params
-    if (row.VariableModifications != null && !row.VariableModifications.toString().trim().isEmpty()) {
-        meta.variablemodifications = row.VariableModifications
+    if (base_row.VariableModifications != null && !base_row.VariableModifications.toString().trim().isEmpty()) {
+        meta.variablemodifications = base_row.VariableModifications
     } else {
         meta.variablemodifications = params.variable_mods
     }
 
-    // Per-file scan ranges (empty string = no flags passed, DIA-NN auto-detects)
-    meta.ms1minmz = row.MS1MinMz?.toString()?.trim() ?: ""
-    meta.ms1maxmz = row.MS1MaxMz?.toString()?.trim() ?: ""
-    meta.ms2minmz = row.MS2MinMz?.toString()?.trim() ?: ""
-    meta.ms2maxmz = row.MS2MaxMz?.toString()?.trim() ?: ""
-
-    enzymes += row.Enzyme
-    if (enzymes.size() > 1) {
-        log.error("Currently only one enzyme is supported for the whole experiment. Specified was '${enzymes}'. Check or split your SDRF.")
-        log.error(filestr)
-        exit(1)
-    }
-
-    // Check for duplicate files
-    if (filestr in files) {
-        log.error("Currently only one DIA-NN setting per file is supported for the whole experiment. ${filestr} has multiple entries in your SDRF. Consider splitting your design into multiple experiments.")
-        exit(1)
-    }
-    files += filestr
+    meta.ms1minmz = base_row.MS1MinMz?.toString()?.trim() ?: ""
+    meta.ms1maxmz = base_row.MS1MaxMz?.toString()?.trim() ?: ""
+    meta.ms2minmz = base_row.MS2MinMz?.toString()?.trim() ?: ""
+    meta.ms2maxmz = base_row.MS2MaxMz?.toString()?.trim() ?: ""
 
     return [meta, filestr]
-}
+}
\ No newline at end of file

From af505677ffb95a56f2cae4909920cba70cb036da Mon Sep 17 00:00:00 2001
From: yueqixuan <yueqx@foxmail.com>
Date: Wed, 8 Apr 2026 11:02:28 +0800
Subject: [PATCH 28/28] Support multiplexing

---
 subworkflows/local/create_input_channel/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/subworkflows/local/create_input_channel/main.nf b/subworkflows/local/create_input_channel/main.nf
index 577441b..2208eca 100644
--- a/subworkflows/local/create_input_channel/main.nf
+++ b/subworkflows/local/create_input_channel/main.nf
@@ -104,7 +104,7 @@ def create_meta_channel_grouped(String filestr, List rows, Map wrapper) {
     def fixedMods = rows.collect { it.FixedModifications?.toString()?.trim() }.findAll { it }.unique()
     meta.fixedmodifications = fixedMods ? fixedMods[0] : null
 
-    // Validate required SDRF columns 
+    // Validate required SDRF columns
     def requiredColumns = [
         'Label': meta.labelling_type,
         'Enzyme': meta.enzyme,
@@ -182,4 +182,4 @@ def create_meta_channel_grouped(String filestr, List rows, Map wrapper) {
     meta.ms2maxmz = base_row.MS2MaxMz?.toString()?.trim() ?: ""
 
     return [meta, filestr]
-}
\ No newline at end of file
+}