Commit 6524520c authored by lrodrig1's avatar lrodrig1
Browse files

minor changes in samtools_view_sam2bam.nf

parent 8d50ef42
process SAMTOOLS_VIEW_SAM2BAM { process SAMTOOLS_VIEW_SAM2BAM {
tag "samtools view sam2bam" tag { "samtools view sam2bam" }
container 'quay.io/biocontainers/samtools:1.5--2' container 'quay.io/biocontainers/samtools:1.5--2'
input: input:
path input path input
output: output:
path "*.bam", emit: output path "*.bam"
script: script:
def threadsArgument = params.threads_samtools ? "--threads $params.threads_samtools" : "" def threadsArgument = params.threads_samtools ? "--threads $params.threads_samtools" : ""
""" """
name=\$(basename $input) name=\$(basename $input)
outputName=\$(echo \${name%.*}) outputName=\$(echo \${name%.*})
samtools view $threadsArgument -bS $input -o \$outputName.bam samtools view $threadsArgument -bS $input -o \$outputName.bam
""" """
} }
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