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groovy formatting

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kevinmenden 2020-12-17 10:24:48 +01:00
parent 8d3fc30eb3
commit 57ab6dbcbf
2 changed files with 15 additions and 15 deletions
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16
software/bowtie/align/main.nf
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@ -11,11 +11,11 @@ process BOWTIE_ALIGN {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
conda (params.enable_conda ? "bioconda::bowtie=1.3.0 bioconda::samtools=1.10" : null) conda (params.enable_conda ? 'bioconda::bowtie=1.3.0 bioconda::samtools=1.10' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0" container 'https://depot.galaxyproject.org/singularity/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
} else { } else {
container "quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0" container 'quay.io/biocontainers/mulled-v2-ffbf83a6b0ab6ec567a336cf349b80637135bca3:9e14e16c284d6860574cf5b624bbc44c793cb024-0'
} }
input: input:
@ -23,9 +23,9 @@ process BOWTIE_ALIGN {
path index path index
output: output:
tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path('*.bam'), emit: bam
tuple val(meta), path("*.out"), emit: log tuple val(meta), path('*.out'), emit: log
path "bowtie.version.txt", emit: version path 'bowtie.version.txt', emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
@ -39,10 +39,10 @@ process BOWTIE_ALIGN {
--sam \\ --sam \\
-x \$INDEX \\ -x \$INDEX \\
-q \\ -q \\
$unaligned \\ $unaligned \\
$options.args \\ $options.args \\
$endedness \\ $endedness \\
2> ${prefix}.out \\ 2> ${prefix}.out \\
| samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam - | samtools view $options.args2 -@ $task.cpus -bS -o ${prefix}.bam -
bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt bowtie --version | head -n 1 | cut -d" " -f3 > ${software}.version.txt

10
software/bowtie/index/main.nf
View file

@ -11,19 +11,19 @@ process BOWTIE_INDEX {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::bowtie=1.3.0" : null) conda (params.enable_conda ? 'bioconda::bowtie=1.3.0' : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1" container 'https://depot.galaxyproject.org/singularity/bowtie:1.3.0--py38hed8969a_1'
} else { } else {
container "quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1" container 'quay.io/biocontainers/bowtie:1.3.0--py38hed8969a_1'
} }
input: input:
path fasta path fasta
output: output:
path "bowtie", emit: index path 'bowtie', emit: index
path "*.version.txt", emit: version path '*.version.txt', emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)