Migrate to topic channels for versions

CHANGELOG.md

@@ -13,6 +13,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Fixed an issue where stripping the sequence in `SUMMARIZE_RESULTS` did not work for complex modifications [#436](https://github.com/nf-core/mhcquant/pull/436)
 
+### `Changed`
+
+- Migrate to topic channels [#431](https://github.com/nf-core/mhcquant/pull/431)
+
+### `Dependencies`
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `MultiQC`  | 1.31.0      | 1.33.0      |
+| `Nf-core`  | 3.4.1       | 3.5.1       |
+| `openms`   | 3.4.1       | 3.5.0       |
+
 ## 3.1.0 - BlüBa - 07/01/26
 
 ### `Added`

modules.json

@@ -7,67 +7,62 @@
                 "nf-core": {
                     "gunzip": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "96c57dfd98a0641886a67bd449fe33ee2ec0e374",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "5bdb098216aaf5df9c3b6343e6204cd932503c16",
                         "installed_by": ["modules"]
                     },
                     "openms/decoydatabase": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/filefilter": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/idfilter": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
-                        "installed_by": ["modules"]
-                    },
-                    "openms/idmassaccuracy": {
-                        "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/idmerger": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/idripper": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/idscoreswitcher": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/peakpickerhires": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openms/peptideindexer": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "openmsthirdparty/cometadapter": {
                         "branch": "master",
-                        "git_sha": "0c47e4193ddde2c5edbc206b5420cbcbee5c9797",
+                        "git_sha": "ca1cd2456f36c913fb3cfb6bdfbf9d1794fd493b",
                         "installed_by": ["modules"]
                     },
                     "thermorawfileparser": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "daaecc3478d6f6ad9cb8f48ec7d657ab6c67877f",
                         "installed_by": ["modules"]
                     }
                 }

modules/local/easypqp/convert/main.nf

@@ -14,7 +14,7 @@ process EASYPQP_CONVERT {
     output:
     tuple val(meta), path("*.psmpkl") , emit: psmpkl
     tuple val(meta), path("*.peakpkl"), emit: peakpkl
-    path "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('easypqp'), eval("easypqp --version 2>&1 | grep -oP '(?<=easypqp, version )\\d+\\.\\d+\\.\\d+'"), emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,11 +32,6 @@ process EASYPQP_CONVERT {
         --spectra $spectra \\
         --unimod $unimod \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        easypqp: \$(easypqp --version 2>&1 | grep -oP '(?<=easypqp, version )\\d+\\.\\d+\\.\\d+')
-    END_VERSIONS
     """
 
     stub:
@@ -49,10 +44,5 @@ process EASYPQP_CONVERT {
 
     touch "${prefix}.psmpkl"
     touch "${prefix}.peakpkl"
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        easypqp: \$(easypqp --version 2>&1 | grep -oP '(?<=easypqp, version )\\d+\\.\\d+\\.\\d+')
-    END_VERSIONS
     """
 }

modules/local/easypqp/library/main.nf

@@ -12,7 +12,7 @@ process EASYPQP_LIBRARY {
 
     output:
     tuple val(meta), path("*.tsv") , emit: tsv
-    path "versions.yml"            , emit: versions
+    tuple val("${task.process}"), val('easypqp'), eval("easypqp --version 2>&1 | grep -oP '(?<=easypqp, version )\\d+\\.\\d+\\.\\d+'"), emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -30,11 +30,6 @@ process EASYPQP_LIBRARY {
         --out ${prefix}_speclib.tsv \
         $args \
         $psmpkl $peakpkl
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        easypqp: \$(easypqp --version 2>&1 | grep -oP '(?<=easypqp, version )\\d+\\.\\d+\\.\\d+')
-    END_VERSIONS
     """
 
     stub:
@@ -46,10 +41,5 @@ process EASYPQP_LIBRARY {
     mkdir -p \$MPLCONFIGDIR \$XDG_CACHE_HOME
 
     touch "${prefix}_speclib.tsv"
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        easypqp: \$(easypqp --version 2>&1 | grep -oP '(?<=easypqp, version )\\d+\\.\\d+\\.\\d+')
-    END_VERSIONS
     """
 }

modules/local/epicore/main.nf

@@ -16,7 +16,7 @@ process EPICORE {
         path "${result_tsv}",                       emit: final_epicore_tsv
         path "epicore_length_distribution.html",    emit: length_dist
         path "epicore_intensity_histogram.html",    emit: intensity_hist
-        path "versions.yml",                        emit: versions
+        tuple val("${task.process}"), val('epicore'), eval("echo \$(epicore --version) | grep 'epicore' | cut -d ' ' -f3 | cut -c2-"), emit: versions, topic: versions
 
     script:
     def args = task.ext.args ?: ''
@@ -32,11 +32,6 @@ process EPICORE {
     # Add epicore statistics to MultiQC general stats table
     wc -l < epitopes.csv | awk '{print \$1 - 1}' > epicores.txt
     awk 'NR==1 {print \$0 ",# Epicores"; next} NR==2 {getline extra < "epicores.txt"; print \$0 "," extra}' $general_stats > _modified_$general_stats
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        epicore: \$(echo \$(epicore --version) | grep 'epicore' | cut -d ' ' -f3 | cut -c2-)
-    END_VERSIONS
     """
 
     stub:
@@ -47,10 +42,5 @@ process EPICORE {
     touch ${prefix}.tsv
     touch epicore_length_distribution.html
     touch epicore_intensity_hist.html
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        epicore: \$(echo \$(epicore --version) | grep 'epicore' | cut -d ' ' -f3 | cut -c2-)
-    END_VERSIONS
     """
 }

modules/local/ms2rescore/main.nf

@@ -17,7 +17,7 @@ process MS2RESCORE {
     tuple val(meta), path("*ms2rescore.idXML") , emit: idxml
     tuple val(meta), path("*feature_names.tsv"), emit: feature_names
     tuple val(meta), path("*.html" )           , optional:true, emit: html
-    path "versions.yml"                        , emit: versions
+    tuple val("${task.process}"), val('MS2Rescore'), eval("echo \"\$(ms2rescore --version 2>&1)\" | grep -oP 'MS²Rescore \\(v\\K[^\\)]+'"), emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,11 +33,6 @@ process MS2RESCORE {
         --output_path ${prefix}.idXML \\
         --processes $task.cpus \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        MS²Rescore: \$(echo \$(ms2rescore --version 2>&1) | grep -oP 'MS²Rescore \\(v\\K[^\\)]+' ))
-    END_VERSIONS
     """
 
     stub:
@@ -47,10 +42,5 @@ process MS2RESCORE {
     touch ${prefix}.idXML
     touch ${meta.id}_feature_names.tsv
     touch ${meta.id}.html
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        MS²Rescore: \$(echo \$(ms2rescore --version 2>&1) | grep -oP 'MS²Rescore \\(v\\K[^\\)]+' ))
-    END_VERSIONS
     """
 }

modules/local/openms/featurefinderidentification/main.nf

@@ -13,38 +13,29 @@ process OPENMS_FEATUREFINDERIDENTIFICATION  {
 
     output:
     tuple val(meta), path("*.featureXML"), emit: featurexml
-    path "versions.yml"                  , emit: versions
+    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | grep -E '^Version' | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//'"), emit: versions_featurefinderidentification, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     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"
+    def args      = quant_fdr
+    args          = args + (task.ext.args ? " ${task.ext.args}" : '')
 
     """
-    FeatureFinderIdentification -in $mzml \\
+    FeatureFinderIdentification \\
+        -in $mzml \\
         -out ${prefix}.featureXML \\
         -threads $task.cpus \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        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}"
 
         """
         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/idconflictresolver/main.nf

@@ -12,7 +12,7 @@ process OPENMS_IDCONFLICTRESOLVER {
 
     output:
     tuple val(meta), path("*.consensusXML"), emit: consensusxml
-    path "versions.yml"                    , emit: versions
+    tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | grep -E '^Version' | sed 's/^.*Version: //; s/-.*\$//' | sed 's/ -*//; s/ .*\$//'"), emit: versions, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,22 +25,12 @@ process OPENMS_IDCONFLICTRESOLVER {
         -in $consensus \\
         -out ${prefix}.consensusXML \\
         -threads $task.cpus
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        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/nf-core/openms/idmassaccuracy/main.nf → modules/local/openms/idmassaccuracy/main.nf

@@ -13,7 +13,7 @@ process OPENMS_IDMASSACCURACY {
     output:
     tuple val(meta), path("*frag_mass_err.tsv") , emit: frag_err
     tuple val(meta), path("*prec_mass_err.tsv") , emit: prec_err, optional: true
-    path "versions.yml"                         , emit: versions
+	tuple val("${task.process}"), val('openms'), eval("FileInfo --help 2>&1 | sed -nE 's/^Version: ([0-9.]+).*/\\1/p'"), emit: versions_openms, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -29,11 +29,6 @@ process OPENMS_IDMASSACCURACY {
         -out_fragment ${prefix}_frag_mass_err.tsv \\
         -threads $task.cpus \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        OpenMS: \$(FileInfo 2>&1 | grep -E '^Version(.*)' | cut -d ' ' -f 2 | cut -d '-' -f 1)
-    END_VERSIONS
     """
 
     stub:
@@ -43,10 +38,5 @@ process OPENMS_IDMASSACCURACY {
     """
     touch ${prefix}_frag_mass_err.tsv
     touch ${prefix}_prec_mass_err.tsv
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        OpenMS: \$(FileInfo 2>&1 | grep -E '^Version(.*)' | cut -d ' ' -f 2 | cut -d '-' -f 1)
-    END_VERSIONS
     """
 }