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Unverified Commit b1f4bf87 authored by Laurent Modolo's avatar Laurent Modolo
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nf_modules: add bedtools for DSL2

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version = "2.25.0"
container_url = "lbmc/bedtools:${version}"
process fasta_from_bed {
container = "${container_url}"
label "big_mem_mono_cpus"
tag "${bed.baseName}"
publishDir "results/fasta/", mode: 'copy'
input:
path fasta
path bed
output:
path "*_extracted.fasta", emit: fasta
script:
"""
bedtools getfasta -name \
-fi ${fasta} -bed ${bed} -fo ${bed.baseName}_extracted.fasta
"""
}
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