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Laurent Modolo authoredLaurent Modolo authored
dedup_sams.nf 507 B
params.sam = "$baseDir/data/sam/*.sam"
log.info "sams files : ${params.sam}"
Channel
.fromPath( params.sam )
.ifEmpty { error "Cannot find any sam files matching: ${params.sam}" }
.map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
.set { sam_files }
process dedup_sam {
tag "$file_id"
cpus 4
input:
set file_id, file(sam) from sam_files
output:
set file_id, "*_dedup.sam*" into dedup_sam_files
script:
"""
samblaster --addMateTags -i ${sam} -o ${file_id}_dedup.sam
"""
}