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amunoz
structuralvariants_poc
Commits
6524520c
Commit
6524520c
authored
Jun 15, 2022
by
lrodrig1
Browse files
minor changes in samtools_view_sam2bam.nf
parent
8d50ef42
Changes
1
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structuralvariants/nextflow/modules/samtools_view_sam2bam.nf
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6524520c
process SAMTOOLS_VIEW_SAM2BAM {
tag "samtools view sam2bam"
tag
{
"samtools view sam2bam"
}
container 'quay.io/biocontainers/samtools:1.5--2'
input:
path input
output:
path "*.bam"
, emit: output
path "*.bam"
script:
def threadsArgument = params.threads_samtools ? "--threads $params.threads_samtools" : ""
"""
name=\$(basename $input)
outputName=\$(echo \${name%.*})
samtools view $threadsArgument -bS $input -o \$outputName.bam
"""
}
\ No newline at end of file
}
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