Sync with nf-core

.github/workflows/awsfulltest.yml

@@ -1,23 +1,25 @@
 name: nf-core AWS full size tests
 # This workflow is triggered on published releases.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
-# It runs the -profile 'test_lfq' on AWS batch
+# It runs the -profiles 'test_lfq' 'test_tmt' and 'test_dia' on AWS batch
 
 on:
   release:
     types: [published]
   workflow_dispatch:
+
 jobs:
   run-tower:
     name: Run AWS full tests
     if: github.repository == 'nf-core/quantms'
     runs-on: ubuntu-latest
+    # Do a full-scale run with data from each acquisition/quantification mode
+    strategy:
+      matrix:
+        mode: ["lfq", "tmt", "dia"]
     steps:
       - name: Launch workflow via tower
         uses: nf-core/tower-action@v3
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_lfq.config` test runs with only one set of parameters
 
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -26,9 +28,9 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/quantms/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/quantms/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/quantms/results-${{ github.sha }}/mode_${{ matrix.mode }}"
             }
-          profiles: test_lfq,aws_tower
+          profiles: test_${{ matrix.mode }},aws_tower
           nextflow_config: |
             process.errorStrategy = 'retry'
             process.maxRetries = 3

CHANGELOG.md

@@ -3,17 +3,17 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [1.0.0] nfcore/quantms - [18/03/2022] - Havana
+## [1.0] nfcore/quantms - [05/02/2022] - Havana
 
 Initial release of nf-core/quantms, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 
 - New pipeline for DDA-LFQ data analysis
 - New pipeline for DDA-ISO data analysis
-- New datasets for DDA-LFQ and DDA-ISO data analsysis
+- New datasets for DDA-LFQ and DDA-ISO data analysis
 - Documentation added for DDA pipeline
-- First pipeline for DIA-LFQ data analsysis
+- First pipeline for DIA-LFQ data analysis
 
 ### `Fixed`
 
@@ -23,16 +23,18 @@ Initial release of nf-core/quantms, created with the [nf-core](https://nf-co.re/
 
 The pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
 
-| Dependency       | Version    |
-| ---------------- | ---------- |
-| `comet`          | 2021010    |
-| `msgf+`          | 2022.01.07 |
-| `openms`         | 2.8.0      |
-| `sdrf-pipelines` | 0.0.21     |
-| `percolator`     | 3.5        |
-| `pmultiqc`       | 0.0.10     |
-| `luciphor`       | 2020_04_03 |
-| `dia-nn`         | 1.8.1      |
-| `msstats`        | 4.2.0      |
+| Dependency            | Version    |
+| --------------------- | ---------- |
+| `thermorawfileparser` | 1.3.4      |
+| `comet`               | 2021010    |
+| `msgf+`               | 2022.01.07 |
+| `openms`              | 2.8.0      |
+| `sdrf-pipelines`      | 0.0.21     |
+| `percolator`          | 3.5        |
+| `pmultiqc`            | 0.0.11     |
+| `luciphor`            | 2020_04_03 |
+| `dia-nn`              | 1.8.1      |
+| `msstats`             | 4.2.0      |
+| `msstatstmt`          | 2.2.0      |
 
 ### `Deprecated`

modules/local/preprocess_expdesign.nf

@@ -1,19 +1,28 @@
 // Fixing file endings only necessary if the experimental design is user-specified
+// TODO can we combine this with another step? Feels like a waste to spawn a worker for this.
+// Maybe the renaming can be done in the rawfileconversion step? Or check if the OpenMS tools
+// accept different file endings already?
 process PREPROCESS_EXPDESIGN {
     label 'process_very_low'
     label 'process_single_thread'
 
+    container "frolvlad/alpine-bash"
+
     input:
     path design
 
     output:
     path "experimental_design.tsv", emit: ch_expdesign
-    path "process_experimental_design.tsv", emit: process_ch_expdesign
+    path "config.tsv", emit: ch_config
 
     script:
 
     """
+    # since we know that we will need to convert from raw to mzML for all tools that need the design (i.e., OpenMS tools)
+    # we edit the design here and change the endings.
     sed 's/.raw\\t/.mzML\\t/I' $design > experimental_design.tsv
-    a=\$(grep -n '^\$' $design | head -n1| awk -F":" '{print \$1}'); sed -e ''"\${a}"',\$d' $design > process_experimental_design.tsv
+
+    # here we extract the filenames and fake an empty config (since the config values will be deduced from the workflow params)
+    a=\$(grep -n '^\$' $design | head -n1| awk -F":" '{print \$1}'); sed -e ''"\${a}"',\$d' $design > config.tsv
     """
 }

modules/local/thermorawfileparser/main.nf

@@ -2,6 +2,7 @@ process THERMORAWFILEPARSER {
     tag "$meta.id"
     label 'process_low'
     label 'process_single_thread'
+    label 'error_retry'
 
     conda (params.enable_conda ? "conda-forge::mono bioconda::thermorawfileparser=1.3.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

subworkflows/local/create_input_channel.nf

@@ -20,14 +20,14 @@ workflow CREATE_INPUT_CHANNEL {
     if (is_sdrf.toString().toLowerCase().contains("true")) {
         SDRFPARSING ( ch_sdrf_or_design )
         ch_versions = ch_versions.mix(SDRFPARSING.out.version)
-        ch_in_design = SDRFPARSING.out.ch_sdrf_config_file
+        ch_config = SDRFPARSING.out.ch_sdrf_config_file
 
         ch_expdesign    = SDRFPARSING.out.ch_expdesign
     } else {
         PREPROCESS_EXPDESIGN( ch_sdrf_or_design )
-        ch_in_design = PREPROCESS_EXPDESIGN.out.process_ch_expdesign
+        ch_config = PREPROCESS_EXPDESIGN.out.ch_config
 
-        ch_expdesign    = PREPROCESS_EXPDESIGN.out.ch_expdesign
+        ch_expdesign = PREPROCESS_EXPDESIGN.out.ch_expdesign
     }
 
     Set enzymes = []
@@ -38,7 +38,7 @@ workflow CREATE_INPUT_CHANNEL {
     wrapper.labelling_type = ""
     wrapper.acquisition_method = ""
 
-    ch_in_design.splitCsv(header: true, sep: '\t')
+    ch_config.splitCsv(header: true, sep: '\t')
             .map { create_meta_channel(it, is_sdrf, enzymes, files, wrapper) }
             .branch {
                 ch_meta_config_dia: it[0].acquisition_method.contains("dia")