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fix index process

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This commit is contained in:
MaxUlysse 2020-01-23 10:19:00 +01:00
parent ad3c14a964
commit a69aebd01b
1 changed files with 3 additions and 4 deletions
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7
tools/samtools/index/main.nf
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@ -7,15 +7,14 @@ process samtools_index {
path(bam) path(bam)
output: output:
path "*.sorted.bam" path "*.bai"
script: script:
def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false' def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : '' def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
""" """
samtools sort $bam \\ samtools index $bam \\
-@ ${task.cpus} ${avail_mem} \\ -@ ${task.cpus} ${avail_mem}
-o ${bam.baseName}.sorted.bam
samtools --version &> v_samtools.txt samtools --version &> v_samtools.txt
""" """