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Update main.nf

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Updated bedtools module with updated container version and upstream/downstream values.
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sruthipsuresh 2020-10-23 08:14:40 -05:00 committed by sruthipsuresh
parent 69f9f1cc89
commit fe2e27c793
1 changed files with 4 additions and 4 deletions
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6
software/bedtools/slopRefseq/main.nf
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@ -17,11 +17,11 @@ process BEDTOOLS_SLOPEREFSEQ {
if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) { if (workflow.containerEngine == 'singularity' && !params.pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0 " container "https://depot.galaxyproject.org/singularity/bedtools:2.29.2--hc088bd4_0 "
} else { } else {
container "quay.io/biocontainers/bedtools:2.27.0--he513fc3" container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
} }
input: input:
path(genome_chrom.sizes) path sizes
tuple val(meta), path(beds) tuple val(meta), path(beds)
output: output:
@ -33,7 +33,7 @@ process BEDTOOLS_SLOPEREFSEQ {
def beds_files = beds.sort() def beds_files = beds.sort()
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
slopBed -i $beds -g ${genome_chrom.sizes} -l 1 -r 10 > {prefix}.sloprefseq.bed slopBed -i $beds -g $sizes -l ${params.upstream} -r {params.downstream} > ${prefix}.sloprefseq.bed
echo $VERSION > ${software}.version.txt echo $VERSION > ${software}.version.txt
""" """
} }