Merge pull request #644 from bigbio/strict_syntax

strict syntax

Author: jpfeuffer

.github/workflows/fix_linting.yml

@@ -11,11 +11,15 @@ jobs:
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
       github.repository == 'bigbio/quantms'
     runs-on: ubuntu-latest
+    permissions:
+      contents: write
+      pull-requests: write
+      issues: write
     steps:
-      # Use the @nf-core-bot token to check out so we can push later
+      # Use the default GITHUB_TOKEN to check out so we can push later
       - uses: actions/checkout@93cb6efe18208431cddfb8368fd83d5badbf9bfd # v5
         with:
-          token: ${{ secrets.nf_core_bot_auth_token }}
+          token: ${{ secrets.GITHUB_TOKEN }}
 
       # indication that the linting is being fixed
       - name: React on comment
@@ -29,7 +33,7 @@ jobs:
       - name: Checkout Pull Request
         run: gh pr checkout ${{ github.event.issue.number }}
         env:
-          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       # Install and run pre-commit
       - uses: actions/setup-python@e797f83bcb11b83ae66e0230d6156d7c80228e7c # v6

conf/modules/modules.config

@@ -18,15 +18,6 @@ process {
     //    saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     //]
 
-    // Set default publish directory for software versions
-    withName: 'BIGBIO_QUANTMS:QUANTMS:CUSTOM_DUMPSOFTWAREVERSIONS' {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: 'copy',
-            pattern: '*_versions.yml'
-        ]
-    }
-
     // Set default publish directory for pmultiqc reports
     withName: 'BIGBIO_QUANTMS:QUANTMS:SUMMARY_PIPELINE' {
         publishDir = [

modules.json

@@ -21,11 +21,6 @@
         "https://github.com/nf-core/modules.git": {
             "modules": {
                 "nf-core": {
-                    "custom/dumpsoftwareversions": {
-                        "branch": "master",
-                        "git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
-                        "installed_by": ["modules"]
-                    },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "8deffd6a402233ebf905c66dbf804bd4c2637946",

modules/local/diann/convert_results/main.nf

@@ -23,15 +23,14 @@ process CONVERT_RESULTS {
     path "*.log", emit: log
     path "versions.yml", emit: versions
 
-    exec:
-        log.info "DIANNCONVERT is based on the output of DIA-NN 1.8.1, 2.0.* and 2.1.*, other versions of DIA-NN don't support mzTab conversion."
 
     script:
     def args = task.ext.args ?: ''
     def dia_params = [meta.fragmentmasstolerance,meta.fragmentmasstoleranceunit,meta.precursormasstolerance,
                         meta.precursormasstoleranceunit,meta.enzyme,meta.fixedmodifications,meta.variablemodifications].join(';')
     def diann2mztab = params.enable_diann_mztab ? "--enable_diann2mztab" : ""
 
+    log.info "DIANNCONVERT is based on the output of DIA-NN 1.8.1, 2.0.* and 2.1.*, other versions of DIA-NN don't support mzTab conversion."
     """
     quantmsutilsc diann2mztab \\
         --folder ./ \\
@@ -42,6 +41,7 @@ process CONVERT_RESULTS {
         --missed_cleavages $params.allowed_missed_cleavages \\
         --qvalue_threshold $params.protein_level_fdr_cutoff \\
         ${diann2mztab} \\
+        $args \\
         2>&1 | tee convert_report.log
 
     cat <<-END_VERSIONS > versions.yml

modules/local/openms/comet/main.nf

@@ -48,11 +48,9 @@ process COMET {
     def isoSlashComet = "0/1"
     if (params.isotope_error_range) {
         def isoRangeComet = params.isotope_error_range.split(",")
-        isoSlashComet = ""
-        for (c in isoRangeComet[0].toInteger()..isoRangeComet[1].toInteger()-1) {
-            isoSlashComet += c + "/"
-        }
-        isoSlashComet += isoRangeComet[1]
+        def range = (isoRangeComet[0].toInteger()..isoRangeComet[1].toInteger()-1).collect { v -> v.toString() }
+        range.add(isoRangeComet[1])
+        isoSlashComet = range.join("/")
     }
     // for consensusID the cutting rules need to be the same. So we adapt to the loosest rules from MSGF
     // TODO find another solution. In ProteomicsLFQ we re-run PeptideIndexer (remove??) and if we
@@ -96,8 +94,8 @@ process COMET {
         -enzyme "${enzyme}" \\
         -isotope_error ${isoSlashComet} \\
         -precursor_charge $params.min_precursor_charge:$params.max_precursor_charge \\
-        -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect { "'$it'" }.join(" ") } \\
-        -variable_modifications ${meta.variablemodifications.tokenize(',').collect { "'$it'" }.join(" ") } \\
+        -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect { mod -> "'$mod'" }.join(" ") } \\
+        -variable_modifications ${meta.variablemodifications.tokenize(',').collect { mod -> "'$mod'" }.join(" ") } \\
         -max_variable_mods_in_peptide $params.max_mods \\
         -precursor_mass_tolerance $meta.precursormasstolerance \\
         -precursor_error_units $meta.precursormasstoleranceunit \\

modules/local/openms/isobaric_analyzer/main.nf

@@ -36,7 +36,7 @@ process ISOBARIC_ANALYZER {
         // Read the matrix file and format it into the command-line format
         // Read the matrix file, skipping lines that start with '#' and process the matrix
         def matrix_lines = new File(params.plex_corr_matrix_file).readLines()
-        .findAll { !it.startsWith('#') && it.trim() } // Skip lines starting with '#' and empty lines
+        .findAll { line -> !line.startsWith('#') && line.trim() } // Skip lines starting with '#' and empty lines
         .drop(1) // Assuming the first non-comment line is a header
         .collect { line ->
             def values = line.split('/')

modules/local/openms/luciphor/main.nf

@@ -20,6 +20,9 @@ process MSGF {
     msgf_jar = ''
     if ((workflow.containerEngine || (task.executor == "awsbatch")) && (task.container.indexOf("biocontainers") > -1 || task.container.indexOf("depot.galaxyproject.org") > -1)) {
         msgf_jar = "-executable \$(find /usr/local/share/msgf_plus-*/MSGFPlus.jar -maxdepth 0)"
+    // TODO session is an undocumented private API of nextflow. Unfortunately there is not other way
+    // of determining if conda was enabled since they did not expose it in the workflow namespace
+    // We could rely on CONDA_PREFIX but this could have been set by other things, not nextflow
     } else if (session.config.conda && session.config.conda.enabled) {
         msgf_jar = "-executable \$(find \$CONDA_PREFIX/share/msgf_plus-*/MSGFPlus.jar -maxdepth 0)"
     }
@@ -83,8 +86,8 @@ process MSGF {
         -tryptic ${msgf_num_enzyme_termini} \\
         -precursor_mass_tolerance $meta.precursormasstolerance \\
         -precursor_error_units $meta.precursormasstoleranceunit \\
-        -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect() { "'${it}'" }.join(" ") } \\
-        -variable_modifications ${meta.variablemodifications.tokenize(',').collect() { "'${it}'" }.join(" ") } \\
+        -fixed_modifications ${meta.fixedmodifications.tokenize(',').collect { mod -> "'${mod}'" }.join(" ") } \\
+        -variable_modifications ${meta.variablemodifications.tokenize(',').collect { mod -> "'${mod}'" }.join(" ") } \\
         -max_mods $params.max_mods \\
         ${il_equiv} \\
         -PeptideIndexing:unmatched_action ${params.unmatched_action} \\

modules/local/openms/luciphor/meta.yml

@@ -21,7 +21,9 @@ process MZML_INDEXING {
 
     """
     mkdir -p out
-    FileConverter -in ${mzmlfile} -out out/${mzmlfile.baseName}.mzML 2>&1 | tee ${mzmlfile.baseName}_mzmlindexing.log
+    FileConverter -in ${mzmlfile} -out out/${mzmlfile.baseName}.mzML \\
+        ${args} \\
+        2>&1 | tee ${mzmlfile.baseName}_mzmlindexing.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":