Bulk update modules to use versions.yml (#739)

* New functions.nf

* Convert code to create versions.yml

* Update meta.yml

* update output channel

* Fix more meta.yml

* Manually update remaining modules

* remove superflous echo

* Fix misformatted meta.yml files

* Fix yaml, was list instead of dict

* fix version for bcftools

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

modules/abacas/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/abacas/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process ABACAS {
 
     output:
     tuple val(meta), path('*.abacas*'), emit: results
-    path '*.version.txt'              , emit: version
+    path "versions.yml"               , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -40,6 +40,9 @@ process ABACAS {
     mv nucmer.filtered.delta ${prefix}.abacas.nucmer.filtered.delta
     mv nucmer.tiling ${prefix}.abacas.nucmer.tiling
     mv unused_contigs.out ${prefix}.abacas.unused.contigs.out
-    echo \$(abacas.pl -v 2>&1) | sed 's/^.*ABACAS.//; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(abacas.pl -v 2>&1 | sed 's/^.*ABACAS.//; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/abacas/meta.yml

@@ -51,7 +51,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
 
 authors:
   - "@joseespinosa"

modules/adapterremoval/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/adapterremoval/main.nf

@@ -1,4 +1,4 @@
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process ADAPTERREMOVAL {
     output:
     tuple val(meta), path('*.fastq.gz'), emit: reads
     tuple val(meta), path('*.log')     , emit: log
-    path "*.version.txt"               , emit: version
+    path "versions.yml"                , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -41,7 +41,10 @@ process ADAPTERREMOVAL {
             --seed 42 \\
             --gzip \\
 
-        AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+        END_VERSIONS
         """
     } else if (!meta.single_end && !meta.collapse) {
         """
@@ -57,7 +60,10 @@ process ADAPTERREMOVAL {
             --seed 42 \\
             --gzip \\
 
-        AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+        END_VERSIONS
         """
     } else {
         """
@@ -73,7 +79,10 @@ process ADAPTERREMOVAL {
             --gzip \\
 
         cat *.collapsed.gz *.collapsed.truncated.gz > ${prefix}.merged.fastq.gz
-        AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(AdapterRemoval --version 2>&1 | sed -e "s/AdapterRemoval ver. //g")
+        END_VERSIONS
         """
     }
 

modules/adapterremoval/meta.yml

@@ -44,7 +44,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 
 authors:
     - "@maxibor"

modules/agrvate/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/agrvate/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process AGRVATE {
     output:
     tuple val(meta), path("${fasta.baseName}-results/${fasta.baseName}-summary.tab"), emit: summary
     path "${fasta.baseName}-results"                                                , emit: results_dir
-    path "*.version.txt"                                                            , emit: version
+    path "versions.yml"                                                             , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -34,6 +34,9 @@ process AGRVATE {
         $options.args \\
         -i $fasta
 
-    echo \$(agrvate -v 2>&1) | sed 's/agrvate //;' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(agrvate -v 2>&1 | sed 's/agrvate //;')
+    END_VERSIONS
     """
 }

modules/agrvate/meta.yml

@@ -41,6 +41,6 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
 authors:
   - "@abhi18av"

modules/allelecounter/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/allelecounter/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process ALLELECOUNTER {
 
     output:
     tuple val(meta), path("*.alleleCount"), emit: allelecount
-    path "*.version.txt"                  , emit: version
+    path "versions.yml"                   , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -36,6 +36,9 @@ process ALLELECOUNTER {
         -b $bam \\
         -o ${prefix}.alleleCount
 
-    alleleCounter --version > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(alleleCounter --version)
+    END_VERSIONS
     """
 }

modules/allelecounter/meta.yml

@@ -42,7 +42,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - alleleCount:
       type: file
       description: Allele count file

modules/arriba/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/arriba/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -26,7 +26,7 @@ process ARRIBA {
     output:
     tuple val(meta), path("*.fusions.tsv")          , emit: fusions
     tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
-    path "*.version.txt"                            , emit: version
+    path "versions.yml"                             , emit: version
 
     script:
     def software  = getSoftwareName(task.process)
@@ -42,6 +42,9 @@ process ARRIBA {
         $blacklist \\
         $options.args
 
-    echo \$(arriba -h | grep 'Version:' 2>&1) |  sed 's/Version:\s//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s//')
+    END_VERSIONS
     """
 }

modules/arriba/meta.yml

@@ -40,7 +40,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - fusions:
       type: file
       description: File contains fusions which pass all of Arriba's filters.

modules/artic/guppyplex/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/artic/guppyplex/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process ARTIC_GUPPYPLEX {
 
     output:
     tuple val(meta), path("*.fastq.gz"), emit: fastq
-    path  "*.version.txt"              , emit: version
+    path  "versions.yml"               , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -36,6 +36,9 @@ process ARTIC_GUPPYPLEX {
         --output ${prefix}.fastq
 
     pigz -p $task.cpus *.fastq
-    echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/artic/guppyplex/meta.yml

@@ -37,7 +37,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
 
 authors:
   - "@joseespinosa"

modules/artic/minion/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/artic/minion/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -40,7 +40,7 @@ process ARTIC_MINION {
     tuple val(meta), path("${prefix}.pass.vcf.gz")                    , emit: vcf
     tuple val(meta), path("${prefix}.pass.vcf.gz.tbi")                , emit: tbi
     tuple val(meta), path("*.json"), optional:true                    , emit: json
-    path  "*.version.txt"                                             , emit: version
+    path  "versions.yml"                                              , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -68,6 +68,9 @@ process ARTIC_MINION {
         $scheme \\
         $prefix
 
-    echo \$(artic --version 2>&1) | sed 's/^.*artic //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(artic --version 2>&1 | sed 's/^.*artic //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/artic/minion/meta.yml

@@ -106,7 +106,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
 
 authors:
   - "@joseespinosa"

modules/bamaligncleaner/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bamaligncleaner/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BAMALIGNCLEANER {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -35,6 +35,9 @@ process BAMALIGNCLEANER {
         -o ${prefix}.bam \\
         ${bam}
 
-    echo \$(bamAlignCleaner --version) | sed 's/.*version //' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bamAlignCleaner --version | sed 's/.*version //')
+    END_VERSIONS
     """
 }

modules/bamaligncleaner/meta.yml

@@ -30,7 +30,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - bam:
       type: file
       description: Sorted BAM/CRAM file

modules/bandage/image/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bandage/image/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BANDAGE_IMAGE {
     output:
     tuple val(meta), path('*.png'), emit: png
     tuple val(meta), path('*.svg'), emit: svg
-    path  '*.version.txt'         , emit: version
+    path  "versions.yml"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -33,6 +33,9 @@ process BANDAGE_IMAGE {
     Bandage image $gfa ${prefix}.png $options.args
     Bandage image $gfa ${prefix}.svg $options.args
 
-    echo \$(Bandage --version 2>&1) | sed 's/^.*Version: //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(Bandage --version 2>&1 | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bandage/image/meta.yml

@@ -38,6 +38,6 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@heuermh"

modules/bbmap/align/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bbmap/align/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BBMAP_ALIGN {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -54,6 +54,9 @@ process BBMAP_ALIGN {
         threads=$task.cpus \\
         -Xmx${task.memory.toGiga()}g
 
-    echo \$(bbversion.sh) > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bbversion.sh)
+    END_VERSIONS
     """
 }

modules/bbmap/align/meta.yml

@@ -42,7 +42,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - bam:
       type: file
       description: BAM file

modules/bbmap/bbduk/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bbmap/bbduk/main.nf

@@ -1,4 +1,4 @@
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BBMAP_BBDUK {
     output:
     tuple val(meta), path('*.fastq.gz'), emit: reads
     tuple val(meta), path('*.log')     , emit: log
-    path '*.version.txt'               , emit: version
+    path "versions.yml"                , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -42,6 +42,9 @@ process BBMAP_BBDUK {
         $options.args \\
         $contaminants_fa \\
         &> ${prefix}.bbduk.log
-    echo \$(bbversion.sh) > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bbversion.sh)
+    END_VERSIONS
     """
 }

modules/bbmap/bbduk/meta.yml

@@ -42,7 +42,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - log:
       type: file
       description: Bbduk log file

modules/bbmap/index/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bbmap/index/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BBMAP_INDEX {
 
     output:
     path 'ref'                    , emit: index
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -34,6 +34,9 @@ process BBMAP_INDEX {
         threads=$task.cpus \\
         -Xmx${task.memory.toGiga()}g
 
-    echo \$(bbversion.sh) > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bbversion.sh)
+    END_VERSIONS
     """
 }

modules/bbmap/index/meta.yml

@@ -23,7 +23,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - db:
       type: directory
       description: Directory with index files

modules/bcftools/concat/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/concat/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BCFTOOLS_CONCAT {
 
     output:
     tuple val(meta), path("*.gz"), emit: vcf
-    path  "*.version.txt"        , emit: version
+    path  "versions.yml"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -35,6 +35,9 @@ process BCFTOOLS_CONCAT {
         --threads $task.cpus \\
         ${vcfs}
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/concat/meta.yml

@@ -37,6 +37,6 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
   - "@abhi18av"

modules/bcftools/consensus/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/consensus/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BCFTOOLS_CONSENSUS {
 
     output:
     tuple val(meta), path('*.fa'), emit: fasta
-    path  '*.version.txt'        , emit: version
+    path  "versions.yml"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -33,6 +33,9 @@ process BCFTOOLS_CONSENSUS {
     header=\$(head -n 1 ${prefix}.fa | sed 's/>//g')
     sed -i 's/\${header}/${meta.id}/g' ${prefix}.fa
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/consensus/meta.yml

@@ -42,7 +42,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/filter/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/filter/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BCFTOOLS_FILTER {
 
     output:
     tuple val(meta), path("*.gz"), emit: vcf
-    path  "*.version.txt"        , emit: version
+    path  "versions.yml"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -34,6 +34,9 @@ process BCFTOOLS_FILTER {
         $options.args \\
         $vcf
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/filter/meta.yml

@@ -34,7 +34,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/isec/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/isec/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BCFTOOLS_ISEC {
 
     output:
     tuple val(meta), path("${prefix}"), emit: results
-    path  "*.version.txt"             , emit: version
+    path  "versions.yml"              , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -33,6 +33,9 @@ process BCFTOOLS_ISEC {
         $options.args \\
         -p $prefix \\
         *.vcf.gz
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/isec/meta.yml

@@ -42,7 +42,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/merge/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/merge/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BCFTOOLS_MERGE {
 
     output:
     tuple val(meta), path("*.gz"), emit: vcf
-    path  "*.version.txt"        , emit: version
+    path  "versions.yml"         , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -33,6 +33,9 @@ process BCFTOOLS_MERGE {
         --output ${prefix}.vcf.gz \\
         $options.args \\
         *.vcf.gz
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/merge/meta.yml

@@ -40,7 +40,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/mpileup/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/mpileup/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -26,7 +26,7 @@ process BCFTOOLS_MPILEUP {
     tuple val(meta), path("*.gz")      , emit: vcf
     tuple val(meta), path("*.tbi")     , emit: tbi
     tuple val(meta), path("*stats.txt"), emit: stats
-    path  "*.version.txt"              , emit: version
+    path  "versions.yml"               , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -42,6 +42,9 @@ process BCFTOOLS_MPILEUP {
         | bcftools view --output-file ${prefix}.vcf.gz --output-type z $options.args3
     tabix -p vcf -f ${prefix}.vcf.gz
     bcftools stats ${prefix}.vcf.gz > ${prefix}.bcftools_stats.txt
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/mpileup/meta.yml

@@ -46,7 +46,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/norm/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/norm/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BCFTOOLS_NORM {
 
     output:
     tuple val(meta), path("*.gz") , emit: vcf
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -37,6 +37,9 @@ process BCFTOOLS_NORM {
         --threads $task.cpus \\
         ${vcf}
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/norm/meta.yml

@@ -40,6 +40,6 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@abhi18av"

modules/bcftools/query/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/query/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -26,7 +26,7 @@ process BCFTOOLS_QUERY {
 
     output:
     tuple val(meta), path("*.gz") , emit: vcf
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -44,6 +44,9 @@ process BCFTOOLS_QUERY {
         $options.args \\
         ${vcf}
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/query/meta.yml

@@ -56,6 +56,6 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
   - "@abhi18av"

modules/bcftools/reheader/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/reheader/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -25,7 +25,7 @@ process BCFTOOLS_REHEADER {
 
     output:
     tuple val(meta), path("*.vcf.gz"), emit: vcf
-    path "*.version.txt"             , emit: version
+    path "versions.yml"              , emit: version
 
     script:
     def software         = getSoftwareName(task.process)
@@ -42,6 +42,9 @@ process BCFTOOLS_REHEADER {
         -o ${prefix}.vcf.gz \\
         $vcf
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/reheader/meta.yml

@@ -41,7 +41,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - vcf:
       type: file
       description: VCF with updated header

modules/bcftools/stats/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/stats/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,13 +23,16 @@ process BCFTOOLS_STATS {
 
     output:
     tuple val(meta), path("*stats.txt"), emit: stats
-    path  "*.version.txt"              , emit: version
+    path  "versions.yml"               , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
     bcftools stats $options.args $vcf > ${prefix}.bcftools_stats.txt
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/stats/meta.yml

@@ -35,7 +35,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bcftools/view/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bcftools/view/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -26,7 +26,7 @@ process BCFTOOLS_VIEW {
 
     output:
     tuple val(meta), path("*.gz") , emit: vcf
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -46,6 +46,9 @@ process BCFTOOLS_VIEW {
         --threads $task.cpus \\
         ${vcf}
 
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
+    END_VERSIONS
     """
 }

modules/bcftools/view/meta.yml

@@ -57,6 +57,6 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@abhi18av"

modules/bedtools/bamtobed/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/bamtobed/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BEDTOOLS_BAMTOBED {
 
     output:
     tuple val(meta), path("*.bed"), emit: bed
-    path  "*.version.txt"         , emit: version
+    path  "versions.yml"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -35,6 +35,9 @@ process BEDTOOLS_BAMTOBED {
         -i $bam \\
         | bedtools sort > ${prefix}.bed
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/bamtobed/meta.yml

@@ -31,7 +31,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@yuukiiwa"
     - "@drpatelh"

modules/bedtools/complement/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/complement/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BEDTOOLS_COMPLEMENT {
 
     output:
     tuple val(meta), path('*.bed'), emit: bed
-    path  '*.version.txt'         , emit: version
+    path  "versions.yml"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -37,6 +37,9 @@ process BEDTOOLS_COMPLEMENT {
         $options.args \\
         > ${prefix}.bed
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/complement/meta.yml

@@ -35,7 +35,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"

modules/bedtools/genomecov/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/genomecov/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -25,7 +25,7 @@ process BEDTOOLS_GENOMECOV {
 
     output:
     tuple val(meta), path("*.${extension}"), emit: genomecov
-    path  "*.version.txt"                  , emit: version
+    path  "versions.yml"                   , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -38,7 +38,10 @@ process BEDTOOLS_GENOMECOV {
             $options.args \\
             > ${prefix}.${extension}
 
-        bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        END_VERSIONS
         """
     } else {
         """
@@ -49,7 +52,10 @@ process BEDTOOLS_GENOMECOV {
             $options.args \\
             > ${prefix}.${extension}
 
-        bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+        cat <<-END_VERSIONS > versions.yml
+        ${getProcessName(task.process)}:
+            ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+        END_VERSIONS
         """
     }
 }

modules/bedtools/genomecov/meta.yml

@@ -38,7 +38,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"

modules/bedtools/getfasta/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/getfasta/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BEDTOOLS_GETFASTA {
 
     output:
     path "*.fa"         , emit: fasta
-    path "*.version.txt", emit: version
+    path "versions.yml" , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -37,6 +37,9 @@ process BEDTOOLS_GETFASTA {
         -bed $bed \\
         -fo ${prefix}.fa
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/getfasta/meta.yml

@@ -27,7 +27,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bedtools/intersect/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/intersect/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BEDTOOLS_INTERSECT {
 
     output:
     tuple val(meta), path("*.${extension}"), emit: intersect
-    path  '*.version.txt'                  , emit: version
+    path  "versions.yml"                   , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -37,6 +37,9 @@ process BEDTOOLS_INTERSECT {
         $options.args \\
         > ${prefix}.${extension}
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/intersect/meta.yml

@@ -38,7 +38,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"

modules/bedtools/makewindows/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/makewindows/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BEDTOOLS_MAKEWINDOWS {
 
     output:
     tuple val(meta), path("*.tab"), emit: tab
-    path "*.version.txt"          , emit: version
+    path "versions.yml"           , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -37,6 +37,9 @@ process BEDTOOLS_MAKEWINDOWS {
         $options.args \\
         > ${prefix}.tab
 
-    echo \$(bedtools --version) | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/makewindows/meta.yml

@@ -34,7 +34,7 @@ output:
   - version:
       type: file
       description: File containing software version
-      pattern: "*.{version.txt}"
+      pattern: "versions.yml"
   - tab:
       type: file
       description: Windows TAB file (BED or BED-like format)

modules/bedtools/maskfasta/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/maskfasta/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BEDTOOLS_MASKFASTA {
 
     output:
     tuple val(meta), path("*.fa"), emit: fasta
-    path "*.version.txt"         , emit: version
+    path "versions.yml"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -36,6 +36,9 @@ process BEDTOOLS_MASKFASTA {
         -fi $fasta \\
         -bed $bed \\
         -fo ${prefix}.fa
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/maskfasta/meta.yml

@@ -37,7 +37,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@joseespinosa"
     - "@drpatelh"

modules/bedtools/merge/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/merge/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BEDTOOLS_MERGE {
 
     output:
     tuple val(meta), path('*.bed'), emit: bed
-    path  '*.version.txt'         , emit: version
+    path  "versions.yml"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -35,6 +35,9 @@ process BEDTOOLS_MERGE {
         $options.args \\
         > ${prefix}.bed
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/merge/meta.yml

@@ -31,7 +31,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"

modules/bedtools/slop/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/slop/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -24,7 +24,7 @@ process BEDTOOLS_SLOP {
 
     output:
     tuple val(meta), path("*.bed"), emit: bed
-    path  "*.version.txt"         , emit: version
+    path  "versions.yml"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -37,7 +37,10 @@ process BEDTOOLS_SLOP {
         $options.args \\
         > ${prefix}.bed
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 
 }

modules/bedtools/slop/meta.yml

@@ -31,7 +31,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"

modules/bedtools/sort/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}

modules/bedtools/sort/main.nf

@@ -1,5 +1,5 @@
 // Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
+include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
 
 params.options = [:]
 options        = initOptions(params.options)
@@ -23,7 +23,7 @@ process BEDTOOLS_SORT {
 
     output:
     tuple val(meta), path('*.bed'), emit: bed
-    path  '*.version.txt'         , emit: version
+    path  "versions.yml"          , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -35,6 +35,9 @@ process BEDTOOLS_SORT {
         $options.args \\
         > ${prefix}.bed
 
-    bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
+    cat <<-END_VERSIONS > versions.yml
+    ${getProcessName(task.process)}:
+        ${getSoftwareName(task.process)}: \$(bedtools --version | sed -e "s/bedtools v//g")
+    END_VERSIONS
     """
 }

modules/bedtools/sort/meta.yml

@@ -31,7 +31,7 @@ output:
     - version:
         type: file
         description: File containing software version
-        pattern: "*.{version.txt}"
+        pattern: "versions.yml"
 authors:
     - "@Emiller88"
     - "@sruthipsuresh"

modules/bedtools/subtract/functions.nf

@@ -9,6 +9,13 @@ def getSoftwareName(task_process) {
     return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
 }
 
+//
+// Extract name of module from process name using $task.process
+//
+def getProcessName(task_process) {
+    return task_process.tokenize(':')[-1]
+}
+
 //
 // Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
 //
@@ -37,9 +44,13 @@ def getPathFromList(path_list) {
 // Function to save/publish module results
 //
 def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
     def ioptions  = initOptions(args.options)
     def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+
+    // Do not publish versions.yml unless running from pytest workflow
+    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {
+        return null
+    }
     if (ioptions.publish_by_meta) {
         def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta
         for (key in key_list) {
@@ -65,4 +76,3 @@ def saveFiles(Map args) {
         return "${getPathFromList(path_list)}/$args.filename"
     }
 }
-}