Commit cfc8d12a authored by lrodrig1's avatar lrodrig1
Browse files

minor changes in samtools_sort.nf

parent 6524520c
process SAMTOOLS_SORT {
tag "samtools sort"
tag { "samtools sort" }
container 'quay.io/biocontainers/samtools:1.5--2'
input:
path input
output:
path "*.sorted.bam", emit: output
path "*.sorted.bam"
script:
def threadsArgument = params.threads_samtools ? "--threads $params.threads_samtools" : ""
"""
name=\$(basename $input)
outputName=\$(echo \${name%.*})
samtools sort $threadsArgument $input -o \$outputName.sorted.bam
"""
}
\ No newline at end of file
}
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