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