nf-core_modules/tools/samtools/index/main.nf
2020-01-23 10:19:00 +01:00

21 lines
530 B
Text

process samtools_index {
tag "${bam.baseName}"
container 'quay.io/biocontainers/samtools:1.9--h10a08f8_12'
input:
path(bam)
output:
path "*.bai"
script:
def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
"""
samtools index $bam \\
-@ ${task.cpus} ${avail_mem}
samtools --version &> v_samtools.txt
"""
}