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Code Issues Releases Packages Activity

Update manual versioning (#1813)

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Mahesh Binzer-Panchal 2022-06-27 10:35:41 +02:00 committed by GitHub
parent b6fe5d2643
commit 233fa70811
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GPG key ID: 4AEE18F83AFDEB23
55 changed files with 114 additions and 117 deletions
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5
modules/adapterremovalfixprefix/main.nf
View file

@ -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 \\

4
modules/amplify/predict/main.nf
View file

@ -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 \\

3
modules/bamcmp/main.nf
View file

@ -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 \\

4
modules/cmseq/polymut/main.nf
View file

@ -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 \\

4
modules/fargene/main.nf
View file

@ -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 \\

3
modules/fastk/fastk/main.nf
View file

@ -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 \\

3
modules/fastk/histex/main.nf
View file

@ -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 \\

4
modules/gamma/gamma/main.nf
View file

@ -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

3
modules/genescopefk/main.nf
View file

@ -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 \\

4
modules/gtdbtk/classifywf/main.nf
View file

@ -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

5
modules/happy/happy/main.nf
View file

@ -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 \\

5
modules/happy/prepy/main.nf
View file

@ -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 \\

4
modules/hisat2/align/main.nf
View file

@ -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') {

4
modules/hisat2/build/main.nf
View file

@ -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

4
modules/hisat2/extractsplicesites/main.nf
View file

@ -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

4
modules/hmmcopy/gccounter/main.nf
View file

@ -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 \\

5
modules/hmmcopy/generatemap/main.nf
View file

@ -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 \\

5
modules/hmmcopy/mapcounter/main.nf
View file

@ -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 \\

4
modules/hmmcopy/readcounter/main.nf
View file

@ -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 \\

4
modules/homer/annotatepeaks/main.nf
View file

@ -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 \\

4
modules/homer/findpeaks/main.nf
View file

@ -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 \\

3
modules/homer/maketagdirectory/main.nf
View file

@ -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 \\

4
modules/homer/makeucscfile/main.nf
View file

@ -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 \\

4
modules/homer/pos2bed/main.nf
View file

@ -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

4
modules/hpsuissero/main.nf
View file

@ -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

5
modules/ichorcna/createpon/main.nf
View file

@ -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

7
modules/ichorcna/run/main.nf
View file

@ -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 \\

4
modules/krakentools/kreport2krona/main.nf
View file

@ -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} \\

4
modules/krona/ktimporttaxonomy/main.nf
View file

@ -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 \\

5
modules/leehom/main.nf
View file

@ -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 \\

4
modules/mcroni/main.nf
View file

@ -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

5
modules/merquryfk/katcomp/main.nf
View file

@ -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 \\

3
modules/merquryfk/katgc/main.nf
View file

@ -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)

5
modules/merquryfk/merquryfk/main.nf
View file

@ -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 \\

5
modules/merquryfk/ploidyplot/main.nf
View file

@ -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 \\

4
modules/mummer/main.nf
View file

@ -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

4
modules/paraclu/main.nf
View file

@ -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

4
modules/phantompeakqualtools/main.nf
View file

@ -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

4
modules/plasmidfinder/main.nf
View file

@ -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 \\

4
modules/rapidnj/main.nf
View file

@ -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")'

4
modules/seacr/callpeak/main.nf
View file

@ -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 \\

5
modules/seqwish/induce/main.nf
View file

@ -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 \\

4
modules/slimfastq/main.nf
View file

@ -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 \\

4
modules/ssuissero/main.nf
View file

@ -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

4
modules/ucsc/bed12tobigbed/main.nf
View file

@ -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 \\

4
modules/ucsc/bedclip/main.nf
View file

@ -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 \\

4
modules/ucsc/bedgraphtobigwig/main.nf
View file

@ -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 \\

4
modules/ucsc/bigwigaverageoverbed/main.nf
View file

@ -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 \\

5
modules/ucsc/liftover/main.nf
View file

@ -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 \

4
modules/ucsc/wigtobigwig/main.nf
View file

@ -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 \\

5
modules/vardictjava/main.nf
View file

@ -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 \\

4
modules/variantbam/main.nf
View file

@ -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 \\

4
modules/vcf2db/main.nf
View file

@ -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 \\

5
modules/vcf2maf/main.nf
View file

@ -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

4
modules/vcflib/vcfuniq/main.nf
View file

@ -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 \\