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 """ }