Commit ebd95323 authored by lrodrig1's avatar lrodrig1
Browse files

update manta.nf

parent 0f0fc8d7
process MANTA {
tag "manta"
tag { "manta" }
container 'quay.io/biocontainers/manta:1.6.0--py27_0'
input:
tuple path(input), path(bai)
tuple path(index_files), path(fai), path(reference_genome)
path regions
tuple path(bams), path(bais)
path reference_genome
path indexs
path bed
path bed_tbi
val manta_exome
output:
tuple path("*.manta.raw.vcf.gz"), emit: output
script:
def exomeArgument = params.manta_exome ? "--exome" : ""
def exomeArgument = manta_exome ? "--exome" : ""
"""
for i in $input
for i in $bams
do
srr=\$(echo \$i | cut -f 1 -d '.')
configManta.py --bam \$i --referenceFasta $reference_genome --runDir generated\$(echo \$srr) --callRegions $regions $exomeArgument
configManta.py --bam \$i --referenceFasta $reference_genome --runDir generated\$(echo \$srr) --callRegions $bed $exomeArgument
python generated\$(echo \$srr)/runWorkflow.py
mv generated\$(echo \$srr)/results/variants/diploidSV.vcf.gz ./\$(echo \$srr).manta.raw.vcf.gz
cp generated\$(echo \$srr)/results/variants/diploidSV.vcf.gz ./\$(echo \$srr).manta.raw.vcf.gz
done
"""
}
\ No newline at end of file
}
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