Add stubs to all local modules

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).
 
-## v2.3.1 - Oesterberg Hotfix - 2024-03-25
+## v2.3.1 - Bühl - 2024-03-28
 
 ### `Fixed`
 

modules/local/cat_files.nf

@@ -30,4 +30,19 @@ process CAT_FILES {
         cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*BusyBox //; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def fileExt = input[0].name.tokenize("\\.")[-1]
+    def prefix = task.ext.suffix ? "${meta.sample}_${task.ext.suffix}" : "${meta.sample}"
+    def type = fileExt == "tsv" ? "prediction_result" : "prediction_proteins"
+
+    """
+    touch ${prefix}_${type}.${fileExt}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*BusyBox //; s/ .*\$//')
+    END_VERSIONS
+    """
+
 }

modules/local/csvtk_concat.nf

@@ -26,4 +26,14 @@ process CSVTK_CONCAT {
         csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${meta.sample}_prediction_result.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        csvtk: \$(echo \$( csvtk version | sed -e "s/csvtk v//g" ))
+    END_VERSIONS
+    """
 }

modules/local/epytope_check_requested_models.nf

@@ -47,4 +47,17 @@ process EPYTOPE_CHECK_REQUESTED_MODELS {
         epytope: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('epytope').version)"))
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch model_report.txt
+    touch model_warnings.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mhcflurry: \$(echo \$(mhcflurry-predict --version 2>&1 | sed 's/^mhcflurry //; s/ .*\$//') )
+        mhcnuggets: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('mhcnuggets').version)"))
+        epytope: \$(echo \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('epytope').version)"))
+    END_VERSIONS
+    """
 }

modules/local/epytope_generate_peptides.nf

@@ -35,4 +35,16 @@ process EPYTOPE_GENERATE_PEPTIDES {
         python: \$(python --version 2>&1 | sed 's/Python //g')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.suffix ? "${meta.sample}_${task.ext.suffix}" : "${meta.sample}_peptides"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        epytope: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('epytope').version)")
+        python: \$(python --version 2>&1 | sed 's/Python //g')
+    END_VERSIONS
+    """
 }

modules/local/epytope_peptide_prediction.nf

@@ -44,9 +44,10 @@ process EPYTOPE_PEPTIDE_PREDICTION {
 
     def netmhc_paths_string = netmhc_paths.join(",")
     def tools_split = params.tools.split(',')
+    // TODO: Move to nf-validation
     def class1_tools = tools_split.findAll { ! it.matches('.*(?i)(class-2|ii).*') }
     def class2_tools = tools_split.findAll { it.matches('.*(?i)(syf|class-2|ii).*') }
-
+    // TODO: Move to nf-validation
     if (((meta.mhc_class == "I") & class1_tools.empty) | ((meta.mhc_class == "II") & class2_tools.empty)) {
         exit 1, "No tools specified for mhc class ${meta.mhc_class}"
     }
@@ -88,4 +89,21 @@ process EPYTOPE_PEPTIDE_PREDICTION {
         mhcnuggets: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('mhcnuggets').version)")
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${splitted.baseName}.json
+    touch ${splitted.baseName}.tsv
+    touch ${splitted.baseName}.fasta
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version 2>&1 | sed 's/Python //g')
+        epytope: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('epytope').version)")
+        pandas: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('pandas').version)")
+        pyvcf: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('PyVCF3').version)")
+        mhcflurry: \$(mhcflurry-predict --version 2>&1 | sed 's/^mhcflurry //; s/ .*\$//')
+        mhcnuggets: \$(python -c "import pkg_resources; print(pkg_resources.get_distribution('mhcnuggets').version)")
+    END_VERSIONS
+    """
 }

modules/local/external_tools_import.nf

@@ -83,4 +83,14 @@ process EXTERNAL_TOOLS_IMPORT {
         ${toolname}: ${toolversion}
     END_VERSIONS
     """
+
+    stub:
+    """
+    mkdir "${toolname}"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ${toolname}: ${toolversion}
+    END_VERSIONS
+    """
 }

modules/local/get_prediction_versions.nf

@@ -32,6 +32,17 @@ process GET_PREDICTION_VERSIONS {
         done
     fi
     """
+
+    stub:
+    """
+    touch versions.csv
+
+    cat <<-END_VERSIONS > versions.csv
+    mhcflurry: \$(mhcflurry-predict --version 2>&1 | sed 's/^mhcflurry //; s/ .*\$//')
+    mhcnuggets: \$(python -c "import pkg_resources; print('mhcnuggets' + pkg_resources.get_distribution('mhcnuggets').version)" | sed 's/^mhcnuggets//; s/ .*\$//' )
+    epytope: \$(python -c "import pkg_resources; print('epytope' + pkg_resources.get_distribution('epytope').version)" | sed 's/^epytope//; s/ .*\$//')
+    END_VERSIONS
+    """
 }
 
 

modules/local/merge_json.nf

@@ -29,4 +29,14 @@ process MERGE_JSON {
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${meta.sample}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
 }

modules/local/snpsift_split.nf

@@ -25,4 +25,15 @@ process SNPSIFT_SPLIT {
         snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' )
     END_VERSIONS
     """
+
+    stub:
+    """
+    touch ${input_file.baseName}.chr1.vcf
+    touch ${input_file.baseName}.chr2.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        snpsift: \$( echo \$(SnpSift split -h 2>&1) | sed 's/^.*version //' | sed 's/(.*//' | sed 's/t//g' )
+    END_VERSIONS
+    """
 }

modules/local/split_peptides.nf

@@ -29,4 +29,16 @@ process SPLIT_PEPTIDES {
         python: \$(python --version | sed 's/Python //g')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.suffix ? "${peptide.baseName}_${task.ext.suffix}" : "${peptide.baseName}"
+    """
+    touch ${prefix}_1.tsv
+    touch ${prefix}_2.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
+    """
 }

modules/local/variant_split.nf

@@ -29,4 +29,14 @@ process VARIANT_SPLIT {
     END_VERSIONS
     """
 
+    stub:
+    """
+    touch ${input_file.baseName}_1.vcf
+    touch ${input_file.baseName}_2.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        python: \$(python --version 2>&1 | sed 's/Python //g')
+    END_VERSIONS
+    """
 }