Merge pull request #1280 from drpatelh/versions

 Update modules in pipeline template with new versions syntax

nf_core/module-template/modules/main.nf

@@ -52,11 +52,11 @@ process {{ tool_name_underscore|upper }} {
     // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
     {{ 'tuple val(meta), path("*.bam")' if has_meta else 'path "*.bam"' }}, emit: bam
     // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"          , emit: version
+    path "versions.yml"          , emit: versions
 
     script:
     {% if has_meta -%}
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     {%- endif %}
     // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
     //               If the software is unable to output a version number on the command-line then it can be manually specified
@@ -80,7 +80,7 @@ process {{ tool_name_underscore|upper }} {
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        samtools: \$( samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//' )
+        ${getSoftwareName(task.process)}: \$( samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//' )
     END_VERSIONS
     """
 }

nf_core/module-template/modules/meta.yml

@@ -37,9 +37,9 @@ output:
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
   {% endif -%}
-  - version:
+  - versions:
       type: file
-      description: File containing software version
+      description: File containing software versions
       pattern: "versions.yml"
   ## TODO nf-core: Delete / customise this example output
   - bam:

nf_core/pipeline-template/modules.json

@@ -4,13 +4,13 @@
     "repos": {
         "nf-core/modules": {
             "custom/dumpsoftwareversions": {
-                "git_sha": "22ec5c6007159d441585ef54bfa6272b6f93c78a"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "fastqc": {
-                "git_sha": "ab67a1d41b63bf52fd7c147f7f8f6e8d167590b5"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             },
             "multiqc": {
-                "git_sha": "ab67a1d41b63bf52fd7c147f7f8f6e8d167590b5"
+                "git_sha": "7b3315591a149609e27914965f858c9a7e071564"
             }
         }
     }

nf_core/pipeline-template/modules/local/samplesheet_check.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { saveFiles } from './functions'
+include { saveFiles; getProcessName } from './functions'
 
 params.options = [:]
 
@@ -20,12 +20,18 @@ process SAMPLESHEET_CHECK {
     path samplesheet
 
     output:
-    path '*.csv'
+    path '*.csv'       , emit: csv
+    path "versions.yml", emit: versions
 
     script: // This script is bundled with the pipeline, in {{ name }}/bin/
     """
     check_samplesheet.py \\
         $samplesheet \\
         samplesheet.valid.csv
+
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        python: \$(python --version | sed 's/Python //g')
+    END_VERSIONS
     """
 }

nf_core/pipeline-template/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf

@@ -22,9 +22,9 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     path versions
 
     output:
-    path 'software_versions.yml'    , emit: yml
-    path 'software_versions_mqc.yml', emit: mqc_yml
-    path 'versions.yml'             , emit: versions
+    path "software_versions.yml"    , emit: yml
+    path "software_versions_mqc.yml", emit: mqc_yml
+    path "versions.yml"             , emit: versions
 
     script:
     """

nf_core/pipeline-template/modules/nf-core/modules/fastqc/main.nf

@@ -24,19 +24,19 @@ process FASTQC {
     output:
     tuple val(meta), path("*.html"), emit: html
     tuple val(meta), path("*.zip") , emit: zip
-    path  "versions.yml"           , emit: version
+    path  "versions.yml"           , emit: versions
 
     script:
     // Add soft-links to original FastQs for consistent naming in pipeline
-    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     if (meta.single_end) {
         """
         [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
         fastqc $options.args --threads $task.cpus ${prefix}.fastq.gz
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+            ${getSoftwareName(task.process)}: \$( fastqc --version | sed -e "s/FastQC v//g" )
         END_VERSIONS
         """
     } else {
@@ -47,7 +47,7 @@ process FASTQC {
 
         cat <<-END_VERSIONS > versions.yml
         ${getProcessName(task.process)}:
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+            ${getSoftwareName(task.process)}: \$( fastqc --version | sed -e "s/FastQC v//g" )
         END_VERSIONS
         """
     }

nf_core/pipeline-template/modules/nf-core/modules/multiqc/main.nf

@@ -24,16 +24,15 @@ process MULTIQC {
     path "*multiqc_report.html", emit: report
     path "*_data"              , emit: data
     path "*_plots"             , optional:true, emit: plots
-    path "versions.yml"        , emit: version
+    path "versions.yml"        , emit: versions
 
     script:
-    def software = getSoftwareName(task.process)
     """
     multiqc -f $options.args .
 
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+        ${getSoftwareName(task.process)}: \$( multiqc --version | sed -e "s/multiqc, version //g" )
     END_VERSIONS
     """
 }

nf_core/pipeline-template/subworkflows/local/input_check.nf

@@ -12,12 +12,14 @@ workflow INPUT_CHECK {
 
     main:
     SAMPLESHEET_CHECK ( samplesheet )
+        .csv
         .splitCsv ( header:true, sep:',' )
         .map { create_fastq_channels(it) }
         .set { reads }
 
     emit:
-    reads // channel: [ val(meta), [ reads ] ]
+    reads                                     // channel: [ val(meta), [ reads ] ]
+    versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ]
 }
 
 // Function to get list of [ meta, [ fastq_1, fastq_2 ] ]

nf_core/pipeline-template/workflows/pipeline.nf

@@ -67,25 +67,26 @@ def multiqc_report = []
 
 workflow {{ short_name|upper }} {
 
-    ch_software_versions = Channel.empty()
+    ch_versions = Channel.empty()
 
     //
     // SUBWORKFLOW: Read in samplesheet, validate and stage input files
     //
     INPUT_CHECK (
         ch_input
     )
+    ch_versions = ch_versions.mix(INPUT_CHECK.out.versions)
 
     //
     // MODULE: Run FastQC
     //
     FASTQC (
         INPUT_CHECK.out.reads
     )
-    ch_software_versions = ch_software_versions.mix(FASTQC.out.version.first().ifEmpty(null))
+    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
-        ch_software_versions.collectFile()
+        ch_versions.collectFile()
     )
 
     //
@@ -104,8 +105,8 @@ workflow {{ short_name|upper }} {
     MULTIQC (
         ch_multiqc_files.collect()
     )
-    multiqc_report       = MULTIQC.out.report.toList()
-    ch_software_versions = ch_software_versions.mix(MULTIQC.out.version.ifEmpty(null))
+    multiqc_report = MULTIQC.out.report.toList()
+    ch_versions    = ch_versions.mix(MULTIQC.out.versions)
 }
 
 /*