Incorporate suggestions for 2.6.0

.github/CONTRIBUTING.md

@@ -29,7 +29,7 @@ If you're not used to this workflow with git, you can start with some [docs from
 You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:
 
 ```bash
-nf-test test --profile debug,test,docker --verbose
+nextflow run . -profile debug,test,docker --outdir <OUTDIR
 ```
 
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.

.nf-core.yml

@@ -1,2 +1,5 @@
 repository_type: pipeline
 nf_core_version: "2.14.1"
+lint:
+  files_unchanged:
+    - .github/CONTRIBUTING.md

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## v2.6.0dev - [date]
+## v2.6.0 - nfcore/mhcquant "Mr. Bob" - 2024/06/17
 
 ### `Added`
 

README.md

@@ -140,7 +140,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 
 ## Citations
 
-If you use nf-core/mhcquant for your analysis, please cite it using the following doi: [10.5281/zenodo.8427707](https://doi.org/10.5281/zenodo.8427707) and the corresponding manuscript:
+If you use nf-core/mhcquant for your analysis, please cite it using the following doi: [10.5281/zenodo.1569909](https://doi.org/10.5281/zenodo.1569909) and the corresponding manuscript:
 
 > **MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics**
 >

assets/multiqc_config.yml

@@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/mhcquant
 custom_logo_title: "nf-core/mhcquant"
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/tree/dev" target="_blank">nf-core/mhcquant</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/releases/tag/2.6.0" target="_blank">nf-core/mhcquant</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mhcquant/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mhcquant/2.6.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mhcquant-methods-description":
     order: -1000

docs/output.md

@@ -26,7 +26,7 @@ By default (only identification) the `best_search_engine_score[1]` holds the per
 The TSV output file is an alternative output of [OpenMS](https://www.openms.de/) comprising similar information to the mzTab output. The TSV output of identification runs is a simple tab-delimited file holding information about FDR-filtered peptides and currently all values produced by `MS²Rescore`. The TSV file in quantification mode (by using `--quantify`) is more complex and described in more detail below
 
 <details markdown="1">
-<summary>TSV Quant</summary
+<summary>TSV Quant</summary>
 
 MAP contains information about the different mzML files that were provided initially
 

docs/usage.md

@@ -77,9 +77,9 @@ nextflow run nf-core/mhcquant \
   --input 'samplesheet.tsv' \
   --outdir <OUTDIR> \
   --fasta 'SWISSPROT_2020.fasta' \
-  <search parameters> \
+  <SEARCH PARAMS> \
   --peptide_min_length 8 \
---peptide_max_length 14 \
+  --peptide_max_length 14 \
   --ms2pip_model 'Immuno-HCD' \
   -profile docker
 ```

modules.json

@@ -17,32 +17,32 @@
                     },
                     "openms/decoydatabase": {
                         "branch": "master",
-                        "git_sha": "0f4f5205a67d3a90adc8e341cf2b19a16f5cb272",
+                        "git_sha": "bbcad23c681ff85336aef1c41345bc313d921b5d",
                         "installed_by": ["modules"]
                     },
                     "openms/idfilter": {
                         "branch": "master",
-                        "git_sha": "f1a1aa1931d1774a0735e34669d3b455c31f6a0b",
+                        "git_sha": "bbcad23c681ff85336aef1c41345bc313d921b5d",
                         "installed_by": ["modules"]
                     },
                     "openms/idmerger": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "bbcad23c681ff85336aef1c41345bc313d921b5d",
                         "installed_by": ["modules"]
                     },
                     "openms/idripper": {
                         "branch": "master",
-                        "git_sha": "82ae8a2a96e84fffb89b57f1ae8bf35ff4ae5f57",
+                        "git_sha": "bbcad23c681ff85336aef1c41345bc313d921b5d",
                         "installed_by": ["modules"]
                     },
                     "openms/idscoreswitcher": {
                         "branch": "master",
-                        "git_sha": "733023d250311ee76c46d6863a4e056f9855eb5d",
+                        "git_sha": "bbcad23c681ff85336aef1c41345bc313d921b5d",
                         "installed_by": ["modules"]
                     },
                     "openms/peakpickerhires": {
                         "branch": "master",
-                        "git_sha": "4e2cbac1db88f544711e488e552175368ca14588",
+                        "git_sha": "bbcad23c681ff85336aef1c41345bc313d921b5d",
                         "installed_by": ["modules"]
                     },
                     "thermorawfileparser": {

modules/local/ms2rescore.nf

@@ -46,6 +46,8 @@ process MS2RESCORE {
 
     """
     touch ${prefix}.idXML
+    touch ${meta.id}_feature_names.tsv
+    touch ${meta.id}.html
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/openms_cometadapter.nf

@@ -52,4 +52,27 @@ process OPENMS_COMETADAPTER {
             openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def args = task.ext.args ?: ''
+        def prefix = task.ext.prefix ?: "${meta.id}_ms2rescore"
+
+        def mods             = params.fixed_mods != " " ? "-fixed_modifications ${params.fixed_mods.tokenize(',').collect { "'${it}'"}.join(" ")}" : "-fixed_modifications"
+        def params_file      = params.default_params_file_comet != " " ? "-default_params_file ${params.default_params_file_comet}" : ""
+        def xions            = params.use_x_ions ? "-use_X_ions true" : ""
+        def zions            = params.use_z_ions ? "-use_Z_ions true" : ""
+        def aions            = params.use_a_ions ? "-use_A_ions true" : ""
+        def cions            = params.use_c_ions ? "-use_C_ions true" : ""
+        def nlions           = params.use_NL_ions ? "-use_NL_ions true" : ""
+        def remove_precursor = params.remove_precursor_peak ? "-remove_precursor_peak yes" : ""
+
+        """
+        touch ${prefix}.idXML
+        touch  ${prefix}_pin.tsv
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_featurefinderidentification.nf

@@ -34,4 +34,19 @@ process OPENMS_FEATUREFINDERIDENTIFICATION  {
             openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}_${meta.sample}_${meta.condition}"
+        def args             = task.ext.args  ?: ''
+        def quant_fdr        = params.quantification_fdr ? "-id $id_int -id_ext $id_ext -svm:min_prob ${params.quantification_min_prob}" : "-id $id_ext"
+        args = args + " $quant_fdr"
+
+        """
+        touch ${prefix}.featureXML
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_featurelinkerunlabeledkd.nf

@@ -22,12 +22,24 @@ process OPENMS_FEATURELINKERUNLABELEDKD {
 
         """
         FeatureLinkerUnlabeledKD -in $features \\
-            -out '${prefix}.consensusXML' \\
+            -out ${prefix}.consensusXML \\
             -threads $task.cpus
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}_all_features_merged"
+
+        """
+        touch ${prefix}.consensusXML
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_filefilter.nf

@@ -30,4 +30,16 @@ process OPENMS_FILEFILTER {
             openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${mzml.baseName}_filtered"
+
+        """
+        touch ${prefix}.mzML
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_idconflictresolver.nf

@@ -30,4 +30,16 @@ process OPENMS_IDCONFLICTRESOLVER {
             openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}_resolved"
+
+        """
+        touch ${prefix}.consensusXML
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_mapaligneridentification.nf

@@ -31,4 +31,18 @@ process OPENMS_MAPALIGNERIDENTIFICATION {
             openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def out_names        = idxmls.collect { it.baseName.replace('_fdr_filtered','')+'.trafoXML' }.join(' ')
+        def args             = task.ext.args  ?: ''
+
+        """
+        touch test1.consensusXML
+        touch test2.consensusXML
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_maprttransformer.nf

@@ -32,4 +32,17 @@ process OPENMS_MAPRTTRANSFORMER {
             openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}"
+        def fileExt          = alignment_file.collect { it.name.tokenize("\\.")[1] }.join(' ')
+
+        """
+        touch ${prefix}.${fileExt}
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_mztabexporter.nf

@@ -32,4 +32,17 @@ process OPENMS_MZTABEXPORTER {
             openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}"
+        def args             = task.ext.args  ?: ''
+
+        """
+        touch ${prefix}.mzTab
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_peptideindexer.nf

@@ -33,4 +33,16 @@ process OPENMS_PEPTIDEINDEXER {
             openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}_${meta.sample}_${meta.condition}_idx"
+
+        """
+        touch ${prefix}.idXML
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_percolatoradapter.nf

@@ -32,4 +32,17 @@ process OPENMS_PERCOLATORADAPTER {
             openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}_pout"
+        def args             = task.ext.args  ?: ''
+
+        """
+        touch ${prefix}.idXML
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms-thirdparty: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_psmfeatureextractor.nf

@@ -36,4 +36,18 @@ process OPENMS_PSMFEATUREEXTRACTOR {
             openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}_psm"
+        def args             = task.ext.args ?: ''
+        def extra_features = ""
+
+        """
+        touch ${prefix}.idXML
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/openms_textexporter.nf

@@ -34,4 +34,17 @@ process OPENMS_TEXTEXPORTER {
             openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
         END_VERSIONS
         """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}"
+        def args             = task.ext.args  ?: ''
+
+        """
+        touch ${prefix}.tsv
+
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            openms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
 }

modules/local/pyopenms_ionannotator.nf

@@ -20,7 +20,6 @@ process PYOPENMS_IONANNOTATOR {
     script:
         def prefix           = task.ext.prefix ?: "${meta.id}"
         def args             = task.ext.args  ?: ''
-
         def xions            = params.use_x_ions ? "--use_x_ions" : ""
         def zions            = params.use_z_ions ? "--use_z_ions" : ""
         def aions            = params.use_a_ions ? "--use_a_ions" : ""
@@ -38,6 +37,24 @@ process PYOPENMS_IONANNOTATOR {
             $cions
 
 
+        cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            pyopenms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')
+        END_VERSIONS
+        """
+
+    stub:
+        def prefix           = task.ext.prefix ?: "${meta.id}"
+        def args             = task.ext.args  ?: ''
+        def xions            = params.use_x_ions ? "--use_x_ions" : ""
+        def zions            = params.use_z_ions ? "--use_z_ions" : ""
+        def aions            = params.use_a_ions ? "--use_a_ions" : ""
+        def cions            = params.use_c_ions ? "--use_c_ions" : ""
+
+        """
+        touch ${prefix}_all_peaks.tsv
+        touch ${prefix}_matching_ions.tsv
+
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
             pyopenms: \$(echo \$(FileInfo --help 2>&1) | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//')