Merge pull request #152 from daichengxin/dev

pull nf-core and update pmultiqc

README.md

@@ -1,4 +1,4 @@
-# ![nf-core/quantms](docs/images/nf-core/quantms_logo_light.png#gh-light-mode-only) ![nf-core/quantms](docs/images/nf-core/quantms_logo_dark.png#gh-dark-mode-only)
+# ![nf-core/quantms](docs/images/nf-core-quantms_logo_light.png#gh-light-mode-only) ![nf-core/quantms](docs/images/nf-core-quantms_logo_dark.png#gh-dark-mode-only)
 
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@@ -77,7 +77,7 @@ DIA-LFQ:
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
    ```console
-   nextflow run nf-core/quantms -profile test,YOURPROFILE --input project.sdrf.tsv --database protein.fasta
+   nextflow run nf-core/quantms -profile test,YOURPROFILE --input project.sdrf.tsv --database protein.fasta --outdir <OUTDIR>
    ```
 
    Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
@@ -97,7 +97,7 @@ DIA-LFQ:
    <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
    ```console
-   nextflow run nf-core/quantms -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input project.sdrf.tsv --database database.fasta
+   nextflow run nf-core/quantms -profile <docker/singularity/podman/shifter/charliecloud/conda/institute> --input project.sdrf.tsv --database database.fasta --outdir <OUTDIR>
    ```
 
 ## Documentation

conf/dev.config

@@ -1,11 +1,15 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running with nightly dev containers
- * -------------------------------------------------
- * Only overwrites the container. See dev/ folder for building instructions.
- * Use as follows:
- *   nextflow run nf-core/quantms -profile dev,<docker/singularity>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running with nightly dev. containers (mainly for OpenMS)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Only overwrites the container. E.g. uses the OpenMS nightly executable and thirdparty
+    containers. TODO Currently does nothing, we need to set it up.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test,<docker/singularity> [--outdir <OUTDIR>]
+
+-------------------------------------------------------------------------------------------
+*/
 
 params {
     config_profile_name = 'Development profile'

conf/modules.config

@@ -160,8 +160,8 @@ process {
         ]
     }
 
-    // EPIFILTER
-    withName: 'NFCORE_QUANTMS:QUANTMS:TMT:.*:EPIFILTER' {
+    // IDFILTER on PROTEIN LEVEL
+    withName: 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEININFERENCE:IDFILTER' {
         ext.args    = [
             "-score:prot \"$params.protein_level_fdr_cutoff\"",
             "-delete_unreferenced_peptide_hits",
@@ -175,27 +175,22 @@ process {
         ]
     }
 
-    //IDCONFLICTRESOLVER
-    withName: 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEINQUANT:IDCONFLICTRESOLVER' {
-        ext.args    = "-debug $params.conflict_resolver_debug"
-    }
-
-    //PROTEINQUANTIFIER
+    // PROTEINQUANTIFIER
     withName: 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEINQUANT:PROTEINQUANTIFIER' {
-        ext.args    = "-debug $params.proteinquant_debug"
+        ext.args    = "-debug 0"
     }
 
-    // MSstatsConverter
+    // MSSTATSCONVERTER
     withName: 'NFCORE_QUANTMS:QUANTMS:TMT:PROTEINQUANT:MSSTATSCONVERTER' {
-        ext.args    = "-debug $params.msstatsconverter_debug"
+        ext.args    = "-debug 0"
     }
 }
 
-if (params.protein_inference_bayesian) {
+if (params.protein_inference_method == "bayesian") {
     process {
         // EPIFANY
         withName: 'NFCORE_QUANTMS:QUANTMS:.*:EPIFANY' {
-            ext.args    = "-debug $params.protein_inference_debug"
+            ext.args    = "-keep_best_psm_only false -debug $params.protein_inference_debug"
             publishDir  = [
                 path: { "${params.outdir}/epifany" },
                 mode: params.publish_dir_mode,
@@ -221,16 +216,6 @@ if (params.protein_inference_bayesian) {
 
 process {
 
-    // INDEXPEPTIDES
-    withName: 'NFCORE_QUANTMS:QUANTMS:.*:INDEXPEPTIDES' {
-        publishDir  = [
-            path: { "${params.outdir}/indexpeptides" },
-            mode: params.publish_dir_mode,
-            pattern: '*.log',
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     // IDFILTER
     withName: 'NFCORE_QUANTMS:QUANTMS:.*:ID:PSMFDRCONTROL:IDFILTER' {
         ext.args    = "-score:pep \"$params.psm_pep_fdr_cutoff\""
@@ -244,7 +229,7 @@ process {
 
     // PROTEOMICSLFQ
     withName: 'NFCORE_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ' {
-        ext.args    = "-debug $params.inf_quant_debug"
+        ext.args    = "-debug $params.plfq_debug"
     }
 
     // DIA-NN

conf/test.config

@@ -1,24 +1,26 @@
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Nextflow config file for running minimal tests
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (ISO)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/quantms -profile test,<docker/singularity>
+        nextflow run nf-core/quantms -profile test,<docker/singularity> [--outdir <OUTDIR>]
 
-----------------------------------------------------------------------------------------
+-------------------------------------------------------------------------------------------
 */
 
 params {
-    config_profile_name        = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile DDA ISO'
+    config_profile_description = 'Minimal test dataset to check pipeline function of the isotopic labelling branch of the pipeline'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2
     max_memory = '6.GB'
     max_time   = '6.h'
 
+    outdir = "./results_iso"
+
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'
 

conf/test_dia.config

@@ -1,20 +1,26 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/quantms -profile test,<docker/singularity/podman>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (DIA)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_dia,<docker/singularity> [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
 
 params {
-    config_profile_name = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile for DIA'
+    config_profile_description = 'Minimal test dataset to check pipeline function for the data-independent acquisition pipeline branch.'
+
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = 6.GB
     max_time = 48.h
 
+    outdir = './results_dia'
+
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/PXD026600/PXD026600.sdrf.tsv'
     database = 'ftp://massive.ucsd.edu/MSV000087597/sequence/REF_EColi_K12_UPS1_combined.fasta'

conf/test_full.config

@@ -5,14 +5,16 @@
     Defines input files and everything required to run a full size pipeline test.
 
     Use as follows:
-        nextflow run nf-core/quantms -profile test_full,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/quantms -profile test_full,<docker/singularity> [--outdir <OUTDIR>]
 
 ----------------------------------------------------------------------------------------
 */
 
 params {
-    config_profile_name        = 'Full test profile'
-    config_profile_description = 'Full test dataset to check pipeline function and sanity of results'
+    config_profile_name        = 'Full test profile DDA ISO'
+    config_profile_description = 'Full test dataset in isotopic labelling mode to check pipeline function and sanity of results'
+
+    outdir = "./results_iso_full"
 
     // Input data for full size test
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'

conf/test_lfq.config

@@ -1,20 +1,26 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/quantms -profile test,<docker/singularity/podman>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (LFQ)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_lfq,<docker/singularity> [--outdir <OUTDIR>]
+
+------------------------------------------------------------------------------------------------
+*/
 
 params {
-    config_profile_name = 'Test profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function'
+    config_profile_name        = 'Test profile for DDA LFQ'
+    config_profile_description = 'Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline'
+
     // Limit resources so that this can run on GitHub Actions
     max_cpus = 2
     max_memory = 6.GB
     max_time = 48.h
 
+    outdir = "./results_lfq"
+
     // Input data
     labelling_type = "label free sample"
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci/BSA/BSA_design_urls.tsv'
@@ -25,5 +31,5 @@ params {
     enable_qc = true
     add_triqler_output = true
     protein_level_fdr_cutoff = 1.0
-    acqusition_method = "dda"
+    acquisition_method = "dda"
 }

conf/test_localize.config

@@ -1,22 +1,26 @@
 /*
- * -------------------------------------------------
- *  Nextflow config file for running tests with
- *  modification localization
- * -------------------------------------------------
- * Defines bundled input files and everything required
- * to run a fast and simple test. Use as follows:
- *   nextflow run nf-core/quantms -profile test_localize,<docker/singularity/podman>
- */
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running minimal tests (LFQ) with mod. localization
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a fast and simple test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_localize,<docker/singularity> [--outdir <OUTDIR>]
+
+----------------------------------------------------------------------------------------------------
+*/
 
 params {
-    config_profile_name = 'Test phospho-localization profile'
-    config_profile_description = 'Minimal test dataset to check pipeline function for phospho-localization, SDRF parsing and ConsensusID.'
+    config_profile_name        = 'Test PTM-localization profile'
+    config_profile_description = 'Minimal test dataset to check pipeline function for PTM-localization, SDRF parsing and ConsensusID.'
 
     // Limit resources so that this can run on Travis
     max_cpus = 2
     max_memory = 6.GB
     max_time = 1.h
 
+    outdir = "./results_localize"
+
     // Input data
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/proteomicslfq/testdata/phospho/test_phospho.sdrf'
     database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/lfq_ci_phospho/pools_crap_targetdecoy.fasta'

modules/local/diannsearch/main.nf

@@ -12,9 +12,9 @@ process DIANNSEARCH {
     file(diann_config)
 
     output:
-    path "report.tsv", emit: report
-    path "report.stats.tsv", emit: report_stat
-    path "report.log.txt", emit: log
+    path "diann_report.tsv", emit: report
+    path "diann_report.stats.tsv", emit: report_stat
+    path "diann_report.log.txt", emit: log
     path "versions.yml", emit: version
     path "*.tsv"
 
@@ -51,13 +51,14 @@ process DIANNSEARCH {
             ${mbr} \\
             --reannotate \\
             ${normalize} \\
+            --out diann_report.tsv \\
             --verbose $params.diann_debug \\
             > diann.log
 
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DIA-NN: 1.8.0
+        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
     END_VERSIONS
     """
 }

modules/local/diannsearch/meta.yml

@@ -30,15 +30,15 @@ output:
   - report:
       type: file
       description: Main report file. A text table containing precursor and protein IDs, as well as plenty of associated information. Most column names are self-explanatory.
-      pattern: "report.tsv"
+      pattern: "diann_report.tsv"
   - report_stat:
       type: file
       description: Contains a number of QC metrics which can be used for data filtering, e.g. to exclude failed runs, or as a readout for method optimization.
-      pattern: "report.stats.tsv"
+      pattern: "diann_report.stats.tsv"
   - log:
       type: file
       description: DIA-NN log file
-      pattern: "report.log.txt"
+      pattern: "diann_report.log.txt"
   - version:
       type: file
       description: File containing software version

modules/local/librarygeneration/main.nf

@@ -51,7 +51,7 @@ process LIBRARYGENERATION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        DIA-NN: 1.8.0
+        DIA-NN: \$(diann 2>&1 | grep "DIA-NN" | grep -oP "(\\d*\\.\\d+\\.\\d+)|(\\d*\\.\\d+)")
     END_VERSIONS
     """
 }

modules/local/librarygeneration/meta.yml

@@ -45,4 +45,4 @@ output:
       description: File containing software version
       pattern: "*.{version.txt}"
 authors:
-  - "@Chengxin Dai"
+  - "@daichengxin"

modules/local/openms/consensusid/main.nf

@@ -2,11 +2,12 @@ process CONSENSUSID {
     label 'process_medium'
     // TODO could be easily parallelized
     label 'process_single_thread'
+    label 'openms'
 
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     tuple val(meta), path(id_file), val(qval_score)

modules/local/openms/decoydatabase/main.nf

@@ -1,9 +1,11 @@
 process DECOYDATABASE {
     label 'process_very_low'
+    label 'openms'
+
     conda (params.enable_conda ? "openms::openms=2.8.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:2.8.0--h9ee0642_0' :
-        'quay.io/biocontainers/openms-thirdparty:2.8.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/openms:2.8.0--h7ca0330_1' :
+        'quay.io/biocontainers/openms:2.8.0--h7ca0330_1' }"
 
     input:
     path(db_for_decoy)