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Unverified Commit a12e9229 authored by Laurent Modolo's avatar Laurent Modolo
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nf_modules: masc2 add DSL2

parent 829ff319
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version = "2.1.2"
container_url = "lbmc/macs2:${version}"
process peak_calling {
container = "${container_url}"
label "big_mem_multi_cpus"
tag "${file_id}"
publishDir "results/peak_calling/${file_id}", mode: 'copy'
input:
tuple val(file_id), path(bam_ip), path(bam_control)
output:
path "*", emit: peak
path "*_report.txt", emit: report
script:
/* remove --nomodel option for real dataset */
"""
macs2 callpeak \
--treatment ${file_ip} \
--call-summits "True"\
--control ${file_control} \
--keep-dup "auto" \
--name ${file_id} \
--gsize ${params.genome_size} 2> \
${file_ip}_macs2_report.txt
if grep -q "ERROR" ${file_ip}_macs2_report.txt; then
echo "MACS2 error"
exit 1
fi
"""
}
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