Commit 7ffd0851 authored by Acivico's avatar Acivico
Browse files

Update manta

parent 0ae880d7
......@@ -142,6 +142,7 @@ workflow {
SUB_CNV_MANTA (
SUB_BAM_FILTERING.out,
samples,
reference_fasta,
indexFiles,
bed,
manta_filter_script,
......@@ -151,7 +152,7 @@ workflow {
params.manta_min_len,
params.manta_min_q
)
if( params.enable_gridss )
SUB_CNV_GRIDSS (
SUB_BAM_FILTERING.out,
......
......@@ -4,8 +4,10 @@ process MANTA {
input:
tuple path(input), path(bai)
tuple path(index_files), path(fai), path(reference_genome)
path reference_genome
path indexs
path regions
path tbi
output:
tuple path("*.manta.raw.vcf.gz"), emit: output
......@@ -13,13 +15,8 @@ process MANTA {
script:
def exomeArgument = params.manta_exome ? "--exome" : ""
"""
for i in $input
do
srr=\$(echo \$i | cut -f 1 -d '.')
configManta.py --bam \$i --referenceFasta $reference_genome --runDir generated\$(echo \$srr) --callRegions $regions $exomeArgument
python generated\$(echo \$srr)/runWorkflow.py
mv generated\$(echo \$srr)/results/variants/diploidSV.vcf.gz ./\$(echo \$srr).manta.raw.vcf.gz
done
configManta.py --bam $input --referenceFasta $reference_genome --runDir generated --callRegions $regions $exomeArgument
python generated/runWorkflow.py
cp generated/results/variants/diploidSV.vcf.gz ./${input.simpleName}.manta.raw.vcf.gz
"""
}
\ No newline at end of file
......@@ -17,7 +17,6 @@ include {
COLLAPSE as MANTA_MERGE
} from "../modules/collapse"
/*
* Subworkflow cnv_manta
*/
......@@ -26,17 +25,20 @@ workflow SUB_CNV_MANTA {
bams
samples
reference_genome
indexs
bed
max_len
min_len
min_q
manta_filter_script
collapse_script
tbi
main:
MANTA(bams,
reference_genome,
bed)
indexs,
bed,
tbi)
SVTOOLS( MANTA.out )
MANTA_FILTER( manta_filter_script, SVTOOLS.out, samples, max_len, min_len, min_q )
MANTA_FILTER( manta_filter_script, SVTOOLS.out, samples )
MANTA_UNION( MANTA_FILTER.out )
MANTA_MERGE( collapse_script, MANTA_UNION.out )
......
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