Merge pull request #423 from ypriverol/dev

update to openms 3.2.0

.github/workflows/ci.yml

@@ -34,7 +34,8 @@ jobs:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
-        test_profile: ["test_lfq", "test_lfq_sage", "test_dia", "test_localize", "test_tmt", "test_dda_id"]
+        test_profile:
+          ["test_lfq", "test_lfq_sage", "test_dia", "test_localize", "test_tmt", "test_dda_id", "test_tmt_corr"]
         exec_profile: ["docker"]
         exclude:
           - test_profile: test_dia
@@ -72,16 +73,19 @@ jobs:
           echo "$(pwd)/micromamba/bin" >> $GITHUB_PATH
           ./bin/micromamba shell init -s bash
           echo $'channels:\n  - conda-forge\n  - bioconda\n  - defaults\nuse_lockfiles: false' >> ~/.mambarc
+
       - name: Install Singularity with defaults
         if: matrix.exec_profile == 'singularity'
         uses: singularityhub/install-singularity@main
-      - name: Run pipeline with test data in docker profile
-        if: matrix.exec_profile == 'docker'
+
+      - name: Run pipeline with test data in docker/singularity profile
+        if: matrix.exec_profile == 'docker' || matrix.exec_profile == 'singularity'
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
+
       - name: Run pipeline with test data in conda profile (and single-threaded)
         env:
           MAMBA_ROOT_PREFIX: ${{ github.workspace }}/.micromamba
@@ -91,35 +95,37 @@ jobs:
         # Remember that you can parallelise this by using strategy.matrix
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,micromamba --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
-      - name: Run pipeline with test data in singularity profile
-        if: matrix.exec_profile == 'singularity'
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile $TEST_PROFILE,$EXEC_PROFILE --outdir ${TEST_PROFILE}_${EXEC_PROFILE}_results
 
       - name: Gather failed logs
         if: failure() || cancelled()
         run: |
           mkdir failed_logs
           failed=$(grep "FAILED" ${TEST_PROFILE}_${EXEC_PROFILE}_results/pipeline_info/execution_trace.txt | cut -f 2)
           while read -r line ; do cp $(ls work/${line}*/*.log) failed_logs/ | true ; done <<< "$failed"
-      - uses: actions/upload-artifact@v1
+
+      - uses: actions/upload-artifact@v4
         if: failure() || cancelled()
         name: Upload failed logs
         with:
-          name: failed_logs
+          name: failed_logs_${{ matrix.test_profile }}_${{ matrix.exec_profile }}_${{ matrix.NXF_VER }}
+          include-hidden-files: true
           path: failed_logs
-      - uses: actions/upload-artifact@v1
+          overwrite: false
+
+      - uses: actions/upload-artifact@v4
         if: always()
         name: Upload results
         with:
-          name: ${{ env.TEST_PROFILE }}_${{ env.EXEC_PROFILE }}_results
-          path: ${{ env.TEST_PROFILE }}_${{ env.EXEC_PROFILE }}_results
-      - uses: actions/upload-artifact@v1
+          name: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_${{ matrix.NXF_VER }}_results
+          include-hidden-files: true
+          path: ${{ matrix.test_profile }}_${{ matrix.exec_profile }}_results
+          overwrite: false
+
+      - uses: actions/upload-artifact@v4
         if: always()
         name: Upload log
         with:
-          name: nextflow.log
+          name: nextflow_${{ matrix.test_profile }}_${{ matrix.exec_profile }}_${{ matrix.NXF_VER }}.log
+          include-hidden-files: true
           path: .nextflow.log
+          overwrite: false

CHANGELOG.md

@@ -3,11 +3,27 @@
 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).
 
+## [1.4.0] nfcore/quantms - [--/--/----] - Cambridge
+
+### `Added`
+
+- [#423](https://github.com/bigbio/quantms/pull/423) Support for plex Correction matrices for TMT and iTRAQ analytical methods.
+
+### `Changed`
+
+- [#423](https://github.com/bigbio/quantms/pull/423) Updated OpenMS==3.2.0
+
+### `Fixed`
+
+### `Dependencies`
+
+- openms==3.2.0
+
 ## [1.3.0] nfcore/quantms - [08/04/2024] - Santiago de Cuba
 
 ### `Added`
 
-- [#335](https://github.com/bigbio/quantms/pull/335) (Performance improvement) Improvements in DIA pipeline to use random/subset files for library search
+- [#335](https://github.com/bigbio/quantms/pull/335) (Performance improvement) Improvements in a DIA pipeline to use random/subset files for library search
 - [#351](https://github.com/bigbio/quantms/pull/351) Identification workflow for DDA data
 - [#362](https://github.com/bigbio/quantms/pull/362) Introduction to ms2rescore to identification workflow
 - [#374](https://github.com/bigbio/quantms/pull/374) Add msgf+ database indexing step

assets/itraq4plex_default_correction.matrix

@@ -0,0 +1,7 @@
+# comment: itraq4plex from MSnbase
+# comment: https://github.com/lgatto/MSnbase/blob/master/inst/extdata/iTRAQ4plexPurityCorrections.csv
+channel/<-2Da>/<-1Da>/<+1Da>/<+2Da>
+114/0.0/1.0/5.9/0.2
+115/0.0/2.0/5.6/0.1
+116/0.0/3.0/4.5/0.1
+117/0.1/4.0/3.5/0.1

assets/itraq8plex_default_correction.matrix

@@ -0,0 +1,11 @@
+# comment: itraq8plex from MSnbase
+# comment: https://github.com/lgatto/MSnbase/blob/master/inst/extdata/iTRAQ8plexPurityCorrections.csv
+channel/<-2Da>/<-1Da>/<+1Da>/<+2Da>
+113/0.0/2.5/3.0/0.1
+114/0.0/1.0/5.9/0.2
+115/0.0/2.0/5.6/0.1
+116/0.0/3.0/4.5/0.1
+117/0.1/4.0/3.5/0.1
+118/0.1/2.0/3.0/0.1
+119/0.1/2.0/4.0/0.1
+121/0.1/2.0/3.0/0.1

assets/tmt11plex_default_correction.matrix

@@ -0,0 +1,14 @@
+# comment: tmt11plex default from OpenMS
+# comment: Product Number: A37725 Lot Number: ZF395505
+channel/<-2Da>/<-1Da>/<+1Da>/<+2Da>
+126/0.0/0.0/8.6/0.3
+127N/0.0/0.1/7.8/0.1
+127C/0.0/0.8/6.9/0.1
+128N/0.0/7.4/7.4/0.0
+128C/0.0/1.5/6.2/0.2
+129N/0.0/1.5/5.7/0.1
+129C/0.0/2.6/4.8/0.0
+130N/0.0/2.2/4.6/0.0
+130C/0.0/2.8/4.5/0.1
+131N/0.1/2.9/3.8/0.0
+131C/0.0/3.9/2.8/0.0

assets/tmt6plex_90064_XL352952_correction.matrix

@@ -0,0 +1,9 @@
+# comment: https://www.thermofisher.com/order/catalog/product/90064B?SID=srch-srp-90064B
+# comment: Product Number: 90064 Lot Number: XL352952
+channel/<-2Da>/<-1Da>/<+1Da>/<+2Da>
+126/0.0/0.0/8.3/0.3
+127/0.0/0.1/7.8/0.1
+128/0.0/1.3/5.7/0.1
+129/0.0/1.5/5.7/0.1
+130/0.0/3.1/3.6/0.0
+131/0.1/2.9/3.8/0.0

assets/tmt6plex_default_correction.matrix

@@ -0,0 +1,10 @@
+# comment: tmt6plex default in OpenMS
+# comment: https://www.thermofisher.com/order/catalog/product/90061?SID=srch-srp-90061
+# comment: Product Number: 90061 Lot Number: ZE386964
+channel/<-2Da>/<-1Da>/<+1Da>/<+2Da>
+126/0.0/0.0/8.6/0.3
+127/0.0/0.1/7.8/0.1
+128/0.0/1.5/6.2/0.2
+129/0.0/1.5/5.7/0.1
+130/0.0/3.1/3.6/0.0
+131/0.1/2.9/3.8/0.0

assets/tmt6plex_msnbase_correction.matrix

@@ -0,0 +1,9 @@
+# comment: tmt6plex from MSnbase
+# comment: https://github.com/lgatto/MSnbase/blob/master/inst/extdata/TMT6plexPurityCorrections.csv
+channel/<-2Da>/<-1Da>/<+1Da>/<+2Da>
+126/0.0/0.0/6.1/0.0
+127/0.0/0.5/6.7/0.0
+128/0.0/1.1/4.2/0.0
+129/0.0/1.7/4.1/0.0
+130/0.0/1.6/2.1/0.0
+131/0.2/3.2/2.8/0.0

conf/dev.config

@@ -18,7 +18,7 @@ params {
 
 process {
     withLabel: openms {
-        conda = "openms::openms-thirdparty=3.1.0"
+        conda = "openms::openms-thirdparty=3.2.0"
         container = {"${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'ghcr.io/openms/openms-executables-sif:latest' : 'ghcr.io/openms/openms-executables:latest' }"}
     }
 }

conf/modules.config

@@ -180,12 +180,12 @@ process {
     }
 
     // IDFILTER on PROTEIN LEVEL
-    level = params.protein_quant == 'strictly_unique_peptides' ? 'prot' : 'protgroup'
+    level = params.protein_quant == 'strictly_unique_peptides' ? 'prot' : 'proteingroup'
     decoys_present = params.quantify_decoys ? ' ' : '-remove_decoys'
     withName: '.*:TMT:PROTEININFERENCE:IDFILTER' {
         ext.args    = [
             "-score:${level} \"$params.protein_level_fdr_cutoff\"",
-            "-score:pep \"$params.psm_level_fdr_cutoff\"",
+            "-score:psm \"$params.psm_level_fdr_cutoff\"",
             "-delete_unreferenced_peptide_hits",
             "${decoys_present}"
         ].join(' ').trim()
@@ -240,7 +240,7 @@ process {
 
     // IDFILTER
     withName: '.*:ID:PSMFDRCONTROL:IDFILTER' {
-        ext.args    = "-score:pep \"$params.run_fdr_cutoff\""
+        ext.args    = "-score:psm \"$params.run_fdr_cutoff\""
         ext.suffix  = '.idXML'
         publishDir  = [
             path: { "${params.outdir}/idfilter" },
@@ -250,7 +250,7 @@ process {
     }
 
     withName: '.*:DDA_ID:PSMFDRCONTROL:IDFILTER' {
-        ext.args    = "-score:pep \"$params.run_fdr_cutoff\""
+        ext.args    = "-score:psm \"$params.run_fdr_cutoff\""
         ext.suffix  = '.idXML'
         publishDir  = [
             path: { "${params.outdir}/idfilter" },

conf/test_tmt_corr.config

@@ -0,0 +1,35 @@
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Nextflow config file for running full-size tests
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    Defines input files and everything required to run a full size pipeline test.
+
+    Use as follows:
+        nextflow run nf-core/quantms -profile test_tmt,<docker/singularity> [--outdir <OUTDIR>]
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    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"
+
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 48.h
+
+    // Input data for full size test
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/PXD000001.sdrf.tsv'
+
+    database = 'https://raw.githubusercontent.com/nf-core/test-datasets/quantms/testdata/tmt_ci/erwinia_carotovora.fasta'
+    posterior_probabilities = "percolator"
+    search_engines = "comet,msgf"
+    psm_level_fdr_cutoff = 1.0
+    decoy_string = "rev"
+    add_decoys = true
+    protocol = 'TMT'
+    isotope_correction = true
+    plex_corr_matrix_file = 'assets/tmt6plex_default_correction.matrix'
+}