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

minor changes in samtools_view_sam2bam.nf

parent 8d50ef42
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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