Update manual versioning (#1813)

modules/adapterremovalfixprefix/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '0.05'
-
 process ADAPTERREMOVALFIXPREFIX {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::adapterremovalfixprefix=0.0.5" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/adapterremovalfixprefix:0.0.5--hdfd78af_2':
@@ -23,7 +22,7 @@ process ADAPTERREMOVALFIXPREFIX {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     if ("$fastq" == "${prefix}.fq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
-
+    def VERSION = '0.0.5' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     AdapterRemovalFixPrefix \\
         $fastq \\

modules/amplify/predict/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.0.3' // Version information not provided by tool
-
 process AMPLIFY_PREDICT {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::amplify=1.0.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/amplify:1.0.3--py36hdfd78af_0':
@@ -24,6 +23,7 @@ process AMPLIFY_PREDICT {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def custom_model_dir = model_dir ? "-md ${model_dir}" : ""
+    def VERSION = '1.0.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     AMPlify \\
         $args \\

modules/bamcmp/main.nf

@@ -1,7 +1,7 @@
-def VERSION = '2.2'
 process BAMCMP {
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::bamcmp=2.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/bamcmp:2.2--h05f6578_0' :
@@ -21,6 +21,7 @@ process BAMCMP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bamcmp \\
         -1 $sample \\

modules/cmseq/polymut/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.0.4' // Version information not provided by tool on CLI
-
 process CMSEQ_POLYMUT {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::cmseq=1.0.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/cmseq:1.0.4--pyhb7b1952_0' :
@@ -24,6 +23,7 @@ process CMSEQ_POLYMUT {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def fasta_refid = fasta ? "-c $fasta" : ""
     def sortindex = bai ? "" : "--sortindex"
+    def VERSION = '1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     polymut.py \\
         $args \\

modules/fargene/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '0.1' // Version information not provided by tool on CLI
-
 process FARGENE {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::fargene=0.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fargene:0.1--py27h21c881e_4' :
@@ -37,6 +36,7 @@ process FARGENE {
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     fargene \\
         $args \\

modules/fastk/fastk/main.nf

@@ -5,6 +5,7 @@ process FASTK_FASTK {
     if (params.enable_conda) {
         error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
     }
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
 
     input:
@@ -22,7 +23,7 @@ process FASTK_FASTK {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0'
+    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     FastK \\
         $args \\

modules/fastk/histex/main.nf

@@ -5,6 +5,7 @@ process FASTK_HISTEX {
     if (params.enable_conda) {
         error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
     }
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
 
     input:
@@ -20,7 +21,7 @@ process FASTK_HISTEX {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0'
+    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     Histex \\
         $args \\

modules/gamma/gamma/main.nf

@@ -1,9 +1,9 @@
-def VERSION = '2.1' // Version information not provided by tool on CLI
 
 process GAMMA_GAMMA {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::gamma=2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gamma%3A2.1--hdfd78af_0':
@@ -26,7 +26,7 @@ process GAMMA_GAMMA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    def VERSION = '2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     if [[ ${fasta} == *.gz ]]
     then

modules/genescopefk/main.nf

@@ -5,6 +5,7 @@ process GENESCOPEFK {
     if (params.enable_conda) {
         error "Conda environments cannot be used when using the GeneScope tool. Please use docker or singularity containers."
     }
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
 
     input:
@@ -25,7 +26,7 @@ process GENESCOPEFK {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def GENESCOPE_VERSION = '380815c420f50171f9234a0fd1ff426b39829b91' // Git commit id is used instead of GeneScopeFK.R -v as software is not release versioned.
+    def GENESCOPE_VERSION = '380815c420f50171f9234a0fd1ff426b39829b91' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     GeneScopeFK.R \\
         $args \\

modules/gtdbtk/classifywf/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.5.0' // Version information not provided by tool on CLI
-
 process GTDBTK_CLASSIFYWF {
     tag "${meta.assembler}-${meta.id}"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::gtdbtk=1.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gtdbtk:1.5.0--pyhdfd78af_0' :
@@ -31,6 +30,7 @@ process GTDBTK_CLASSIFYWF {
     script:
     def args = task.ext.args ?: ''
     def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
+    def VERSION = '1.5.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     export GTDBTK_DATA_PATH="\${PWD}/database"
     if [ ${pplacer_scratch} != "" ] ; then

modules/happy/happy/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '0.3.14'
-
 process HAPPY_HAPPY {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0':
@@ -23,7 +22,7 @@ process HAPPY_HAPPY {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     hap.py \\
         $truth_vcf \\

modules/happy/prepy/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '0.3.14'
-
 process HAPPY_PREPY {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::hap.py=0.3.14" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hap.py:0.3.14--py27h5c5a3ab_0':
@@ -23,7 +22,7 @@ process HAPPY_PREPY {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    def VERSION = '0.3.14' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     pre.py \\
         $args \\

modules/hisat2/align/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '2.2.0' // Version information not provided by tool on CLI
-
 process HISAT2_ALIGN {
     tag "$meta.id"
     label 'process_high'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::hisat2=2.2.0 bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:0e773bb207600fcb4d38202226eb20a33c7909b6-0' :
@@ -26,6 +25,7 @@ process HISAT2_ALIGN {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
 
     def strandedness = ''
     if (meta.strandedness == 'forward') {

modules/hisat2/build/main.nf

@@ -1,10 +1,9 @@
-def VERSION = '2.2.0' // Version information not provided by tool on CLI
-
 process HISAT2_BUILD {
     tag "$fasta"
     label 'process_high'
     label 'process_high_memory'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' :
@@ -45,6 +44,7 @@ process HISAT2_BUILD {
         log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index."
         log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check."
     }
+    def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     mkdir hisat2
     $extract_exons

modules/hisat2/extractsplicesites/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '2.2.0' // Version information not provided by tool on CLI
-
 process HISAT2_EXTRACTSPLICESITES {
     tag "$gtf"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? 'bioconda::hisat2=2.2.1' : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' :
@@ -21,6 +20,7 @@ process HISAT2_EXTRACTSPLICESITES {
 
     script:
     def args = task.ext.args ?: ''
+    def VERSION = '2.2.0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt
     cat <<-END_VERSIONS > versions.yml

modules/hmmcopy/gccounter/main.nf

@@ -1,8 +1,7 @@
-def VERSION = '0.1.1' // Version information not provided by tool on CLI
-
 process HMMCOPY_GCCOUNTER {
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' :
@@ -20,6 +19,7 @@ process HMMCOPY_GCCOUNTER {
 
     script:
     def args = task.ext.args ?: ''
+    def VERSION = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     gcCounter \\
         $args \\

modules/hmmcopy/generatemap/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '0.1.1'
-
 process HMMCOPY_GENERATEMAP {
     tag '$bam'
     label 'process_long'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7':
@@ -21,7 +20,7 @@ process HMMCOPY_GENERATEMAP {
 
     script:
     def args = task.ext.args ?: ''
-
+    def VERSION = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     # build required indexes
     generateMap.pl -b \\

modules/hmmcopy/mapcounter/main.nf

@@ -1,8 +1,7 @@
-def VERSION = '0.1.1' // Version information not provided by tool on CLI
-
 process HMMCOPY_MAPCOUNTER {
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7':
@@ -20,7 +19,7 @@ process HMMCOPY_MAPCOUNTER {
 
     script:
     def args = task.ext.args ?: ''
-
+    def VERSION = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     mapCounter \\
         $args \\

modules/hmmcopy/readcounter/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '0.1.1' // Version information not provided by tool on CLI
-
 process HMMCOPY_READCOUNTER {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7' :
@@ -22,6 +21,7 @@ process HMMCOPY_READCOUNTER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     readCounter \\
         $args \\

modules/homer/annotatepeaks/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '4.11' // Version information not provided by tool on CLI
-
 process HOMER_ANNOTATEPEAKS {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::homer=4.11" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
@@ -24,6 +23,7 @@ process HOMER_ANNOTATEPEAKS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     annotatePeaks.pl \\
         $peak \\

modules/homer/findpeaks/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '4.11' // Version information not provided by tool on CLI
-
 process HOMER_FINDPEAKS {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
@@ -22,6 +21,7 @@ process HOMER_FINDPEAKS {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
 
     findPeaks \\

modules/homer/maketagdirectory/main.nf

@@ -1,9 +1,9 @@
-def VERSION = '4.11' // Version information not provided by tool on CLI
 
 process HOMER_MAKETAGDIRECTORY {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::homer=4.11 bioconda::samtools=1.11 conda-forge::r-base=4.0.2 bioconda::bioconductor-deseq2=1.30.0 bioconda::bioconductor-edger=3.32.0 anaconda::perl=5.26.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-29293b111ffe5b4c1d1e14c711264aaed6b97b4a:594338b771cacf1623bd27772b5e12825f8835f2-0' :
@@ -24,6 +24,7 @@ process HOMER_MAKETAGDIRECTORY {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     makeTagDirectory \\
         ${prefix}_tagdir \\

modules/homer/makeucscfile/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '4.11' // Version information not provided by tool on CLI
-
 process HOMER_MAKEUCSCFILE {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::homer=4.11=pl526hc9558a2_3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
@@ -22,6 +21,7 @@ process HOMER_MAKEUCSCFILE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     makeUCSCfile \\
         $tagDir \\

modules/homer/pos2bed/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '4.11' // Version information not provided by tool on CLI
-
 process HOMER_POS2BED {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::homer=4.11" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
@@ -22,6 +21,7 @@ process HOMER_POS2BED {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     pos2bed.pl $peaks > ${prefix}.bed
 

modules/hpsuissero/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.0.1' // Version information not provided by tool on CLI
-
 process HPSUISSERO {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::hpsuissero=1.0.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/hpsuissero%3A1.0.1--hdfd78af_0':
@@ -24,6 +23,7 @@ process HPSUISSERO {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def is_compressed = fasta.getName().endsWith(".gz") ? true : false
     def fasta_name = fasta.getName().replace(".gz", "")
+    def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     if [ "$is_compressed" == "true" ]; then
         gzip -c -d $fasta > $fasta_name

modules/ichorcna/createpon/main.nf

@@ -1,8 +1,7 @@
-def VERSION = '0.3.2' // Version information not provided by tool on CLI
-
 process ICHORCNA_CREATEPON {
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' :
@@ -26,7 +25,7 @@ process ICHORCNA_CREATEPON {
     def args = task.ext.args ?: ''
     def centro = centromere ? "--centromere ${centromere}" : ''
     def prefix = task.ext.prefix ?: "PoN"
-
+    def VERSION = '0.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     echo ${wigs} | tr " " "\\n" > wig_files.txt
 

modules/ichorcna/run/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '0.3.2' // Version information not provided by tool on CLI
-
 process ICHORCNA_RUN {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' :
@@ -23,14 +22,14 @@ process ICHORCNA_RUN {
     path "versions.yml"                   , emit: versions
 
     when:
-        task.ext.when == null || task.ext.when
+    task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def pon = panel_of_normals ? "--normalPanel ${panel_of_normals}" : ''
     def centro = centromere ? "--centromere ${centromere}" : ''
-
+    def VERSION = '0.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     runIchorCNA.R --id ${prefix} \\
         $args \\

modules/krakentools/kreport2krona/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.2' // Version information not provided by tool on CLI
-
 process KRAKENTOOLS_KREPORT2KRONA {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::krakentools=1.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
@@ -22,6 +21,7 @@ process KRAKENTOOLS_KREPORT2KRONA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     kreport2krona.py \\
         -r ${kreport} \\

modules/krona/ktimporttaxonomy/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '2.8' // Version information not provided by tool on CLI
-
 process KRONA_KTIMPORTTAXONOMY {
     tag "${meta.id}"
     label 'process_high'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::krona=2.8" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' :
@@ -22,6 +21,7 @@ process KRONA_KTIMPORTTAXONOMY {
 
     script:
     def args = task.ext.args ?: ''
+    def VERSION = '2.8' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     ktImportTaxonomy \\
         $args \\

modules/leehom/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.2.15' // Version information not provided by tool on CLI
-
 process LEEHOM {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::leehom=1.2.15" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/leehom:1.2.15--h29e30f7_1' :
@@ -29,7 +28,7 @@ process LEEHOM {
     script:
     def args = task.ext.args   ?: ''
     prefix   = task.ext.prefix ?: "${meta.id}"
-
+    def VERSION = '1.2.15' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     if (reads.toString().endsWith('.bam')) {
         """
         leeHom \\

modules/mcroni/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.0.4' // Version information not provided by tool on CLI
-
 process MCRONI {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::mcroni=1.0.4" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mcroni%3A1.0.4--pyh5e36f6f_0':
@@ -25,6 +24,7 @@ process MCRONI {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def is_compressed = fasta.getName().endsWith(".gz") ? true : false
     def fasta_name = fasta.getName().replace(".gz", "")
+    def VERSION = '1.0.4' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     if [ "$is_compressed" == "true" ]; then
         gzip -c -d $fasta > $fasta_name

modules/merquryfk/katcomp/main.nf

@@ -5,6 +5,7 @@ process MERQURYFK_KATCOMP {
     if (params.enable_conda) {
         error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
     }
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
 
     input:
@@ -25,8 +26,8 @@ process MERQURYFK_KATCOMP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0'
-    def MERQURY_VERSION = '8f3ab706e4cf4d7b7d1dfe5739859e3ebd26c494'
+    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def MERQURY_VERSION = '8f3ab706e4cf4d7b7d1dfe5739859e3ebd26c494' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     KatComp \\
         $args \\

modules/merquryfk/katgc/main.nf

@@ -5,7 +5,8 @@ process MERQURYFK_KATGC {
     if (params.enable_conda) {
         error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
     }
-    container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0' // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
 
     input:
     tuple val(meta), path(fastk_hist), path(fastk_ktab)

modules/merquryfk/merquryfk/main.nf

@@ -5,6 +5,7 @@ process MERQURYFK_MERQURYFK {
     if (params.enable_conda) {
         error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
     }
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
 
     input:
@@ -35,8 +36,8 @@ process MERQURYFK_MERQURYFK {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0'
-    def MERQURY_VERSION = '8f3ab706e4cf4d7b7d1dfe5739859e3ebd26c494'
+    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def MERQURY_VERSION = '8f3ab706e4cf4d7b7d1dfe5739859e3ebd26c494' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     MerquryFK \\
         $args \\

modules/merquryfk/ploidyplot/main.nf

@@ -5,6 +5,7 @@ process MERQURYFK_PLOIDYPLOT {
     if (params.enable_conda) {
         error "Conda environments cannot be used when using the FastK tool. Please use docker or singularity containers."
     }
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     container 'ghcr.io/nbisweden/fastk_genescopefk_merquryfk:1.0'
 
     input:
@@ -25,8 +26,8 @@ process MERQURYFK_PLOIDYPLOT {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0'
-    def MERQURY_VERSION = '8f3ab706e4cf4d7b7d1dfe5739859e3ebd26c494'
+    def FASTK_VERSION = 'f18a4e6d2207539f7b84461daebc54530a9559b0' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    def MERQURY_VERSION = '8f3ab706e4cf4d7b7d1dfe5739859e3ebd26c494' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     PloidyPlot \\
         $args \\

modules/mummer/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '3.23' // Version information not provided by tool on CLI
-
 process MUMMER {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::mummer=3.23" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mummer:3.23--pl5262h1b792b2_12' :
@@ -27,6 +26,7 @@ process MUMMER {
 
     def is_compressed_query = query.getName().endsWith(".gz") ? true : false
     def fasta_name_query = query.getName().replace(".gz", "")
+    def VERSION = '3.23' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     if [ "$is_compressed_ref" == "true" ]; then
         gzip -c -d $ref > $fasta_name_ref

modules/paraclu/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '10' // Version information not provided by tool on CLI
-
 process PARACLU {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::paraclu=10" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' :
@@ -23,6 +22,7 @@ process PARACLU {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '10' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
 
     awk -F "\t" '{print\$1"\t"\$6"\t"\$2"\t"\$5}' < $bed > ${bed}_4P

modules/phantompeakqualtools/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.2.2' // Version information not provided by tool on CLI
-
 process PHANTOMPEAKQUALTOOLS {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::phantompeakqualtools=1.2.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/phantompeakqualtools:1.2.2--0' :
@@ -25,6 +24,7 @@ process PHANTOMPEAKQUALTOOLS {
     def args   = task.ext.args ?: ''
     def args2  = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.2.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     RUN_SPP=`which run_spp.R`
     Rscript $args -e "library(caTools); source(\\"\$RUN_SPP\\")" -c="$bam" -savp="${prefix}.spp.pdf" -savd="${prefix}.spp.Rdata" -out="${prefix}.spp.out" $args2

modules/plasmidfinder/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '2.1.6' // Version information not provided by tool on CLI
-
 process PLASMIDFINDER {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::plasmidfinder=2.1.6=py310hdfd78af_1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/plasmidfinder:2.1.6--py310hdfd78af_1':
@@ -26,6 +25,7 @@ process PLASMIDFINDER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2.1.6' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     plasmidfinder.py \\
         $args \\

modules/rapidnj/main.nf

@@ -1,8 +1,7 @@
-def VERSION = '2.3.2' // Version information not provided by tool on CLI
-
 process RAPIDNJ {
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::rapidnj=2.3.2 conda-forge::biopython=1.78" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-805c6e0f138f952f9c61cdd57c632a1a263ea990:3c52e4c8da6b3e4d69b9ca83fa4d366168898179-0' :
@@ -21,6 +20,7 @@ process RAPIDNJ {
 
     script:
     def args = task.ext.args ?: ''
+    def VERSION = '2.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     python \\
         -c 'from Bio import SeqIO; SeqIO.convert("$alignment", "fasta", "alignment.sth", "stockholm")'

modules/seacr/callpeak/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.3' // Version information not provided by tool on CLI
-
 process SEACR_CALLPEAK {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' :
@@ -24,6 +23,7 @@ process SEACR_CALLPEAK {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold"
+    def VERSION = '1.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     SEACR_1.3.sh \\
         $bedgraph \\

modules/seqwish/induce/main.nf

@@ -1,11 +1,9 @@
-def VERSION = '0.7.2' // Version information not provided by tool on CLI
-
 process SEQWISH_INDUCE {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? 'bioconda::seqwish=0.7.2' : null)
-
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/seqwish:0.7.2--h2e03b76_0' :
         'quay.io/biocontainers/seqwish:0.7.2--h2e03b76_0' }"
@@ -23,6 +21,7 @@ process SEQWISH_INDUCE {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '0.7.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     seqwish \\
         --threads $task.cpus \\

modules/slimfastq/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '2.04'
-
 process SLIMFASTQ {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::slimfastq=2.04" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/slimfastq:2.04--h87f3376_2':
@@ -22,6 +21,7 @@ process SLIMFASTQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '2.04' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     if (meta.single_end) {
         """
         gzip -d -c '${fastq}' | slimfastq \\

modules/ssuissero/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.0.1' // Version information not provided by tool on CLI
-
 process SSUISSERO {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::ssuissero=1.0.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ssuissero%3A1.0.1--hdfd78af_0':
@@ -24,6 +23,7 @@ process SSUISSERO {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def is_compressed = fasta.getName().endsWith(".gz") ? true : false
     def fasta_name = fasta.getName().replace(".gz", "")
+    def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     if [ "$is_compressed" == "true" ]; then
         gzip -c -d $fasta > $fasta_name

modules/ucsc/bed12tobigbed/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '377' // Version information not provided by tool on CLI
-
 process UCSC_BED12TOBIGBED {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::ucsc-bedtobigbed=377" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-bedtobigbed:377--h446ed27_1' :
@@ -23,6 +22,7 @@ process UCSC_BED12TOBIGBED {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bedToBigBed \\
         $bed \\

modules/ucsc/bedclip/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '377' // Version information not provided by tool on CLI
-
 process UCSC_BEDCLIP {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::ucsc-bedclip=377" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-bedclip:377--h0b8a92a_2' :
@@ -23,6 +22,7 @@ process UCSC_BEDCLIP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bedClip \\
         $bedgraph \\

modules/ucsc/bedgraphtobigwig/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '377' // Version information not provided by tool on CLI
-
 process UCSC_BEDGRAPHTOBIGWIG {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1' :
@@ -23,6 +22,7 @@ process UCSC_BEDGRAPHTOBIGWIG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     bedGraphToBigWig \\
         $bedgraph \\

modules/ucsc/bigwigaverageoverbed/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '377' // Version information not provided by tool on CLI
-
 process UCSC_BIGWIGAVERAGEOVERBED {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::ucsc-bigwigaverageoverbed=377" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-bigwigaverageoverbed:377--h0b8a92a_2' :
@@ -23,6 +22,7 @@ process UCSC_BIGWIGAVERAGEOVERBED {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     // BUG: bigWigAverageOverBed cannot handle ensembl seqlevels style
     """
     bigWigAverageOverBed \\

modules/ucsc/liftover/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '377' // Version information not provided by tool on CLI
-
 process UCSC_LIFTOVER {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::ucsc-liftover=377" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-liftover:377--h0b8a92a_3' :
@@ -24,7 +23,7 @@ process UCSC_LIFTOVER {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     liftOver \\
         $args \

modules/ucsc/wigtobigwig/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '377' // Version information not provided by tool on CLI
-
 process UCSC_WIGTOBIGWIG {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::ucsc-wigtobigwig=377" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/ucsc-wigtobigwig:377--h0b8a92a_2' :
@@ -23,6 +22,7 @@ process UCSC_WIGTOBIGWIG {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '377' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     wigToBigWig \\
         $args \\

modules/vardictjava/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.8.3'
-
 process VARDICTJAVA {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0':
@@ -24,7 +23,7 @@ process VARDICTJAVA {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
+    def VERSION = '1.8.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     vardict-java \\
         $args \\

modules/variantbam/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.4.4a' // Version information not provided by tool on CLI
-
 process VARIANTBAM {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::variantbam=1.4.4a" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/variantbam:1.4.4a--h7d7f7ad_5' :
@@ -22,6 +21,7 @@ process VARIANTBAM {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.4.4a' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     variant \\
         $bam \\

modules/vcf2db/main.nf

@@ -1,9 +1,8 @@
-VERSION = "2020.02.24"
-
 process VCF2DB {
     tag "$meta.id"
     label 'process_medium'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::vcf2db=2020.02.24" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/vcf2db:2020.02.24--hdfd78af_1':
@@ -22,6 +21,7 @@ process VCF2DB {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = "2020.02.24" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     vcf2db.py \\
         $vcf \\

modules/vcf2maf/main.nf

@@ -1,10 +1,9 @@
-def VERSION = '1.6.21'
-
 process VCF2MAF {
 
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::vcf2maf=1.6.21 bioconda::ensembl-vep=106.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/mulled-v2-b6fc09bed47d0dc4d8384ce9e04af5806f2cc91b:305092c6f8420acd17377d2cc8b96e1c3ccb7d26-0':
@@ -26,9 +25,9 @@ process VCF2MAF {
     def args          = task.ext.args   ?: ''
     def prefix        = task.ext.prefix ?: "${meta.id}"
     def vep_cache_cmd = vep_cache       ? "--vep-data $vep_cache" : ""
-
     // If VEP is present, it will find it and add it to commands.
     // If VEP is not present they will be blank
+    def VERSION = '1.6.21' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     if command -v vep &> /dev/null
     then

modules/vcflib/vcfuniq/main.nf

@@ -1,9 +1,8 @@
-def VERSION = '1.0.2' // Version information not provided by tool on CLI
-
 process VCFLIB_VCFUNIQ {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
     conda (params.enable_conda ? "bioconda::vcflib=1.0.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/vcflib:1.0.2--h3198e80_5':
@@ -22,6 +21,7 @@ process VCFLIB_VCFUNIQ {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '1.0.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     vcfuniq \\
         $vcf \\