Commit d349f9ae authored by amunoz's avatar amunoz
Browse files

Manta, svtools and manta_filter fix

parent 7ffd0851
......@@ -140,7 +140,7 @@ workflow {
if( params.enable_manta )
SUB_CNV_MANTA (
SUB_BAM_FILTERING.out,
SUB_BAM_FILTERING.out.collect(),
samples,
reference_fasta,
indexFiles,
......@@ -155,7 +155,7 @@ workflow {
if( params.enable_gridss )
SUB_CNV_GRIDSS (
SUB_BAM_FILTERING.out,
SUB_BAM_FILTERING.out.collect(),
samples,
indexFiles,
blacklist,
......@@ -169,7 +169,7 @@ workflow {
if( params.enable_exomeDepth )
SUB_CNV_EXOMEDEPTH (
SUB_BAM_FILTERING.out,
SUB_BAM_FILTERING.out.collect(),
samples,
indexFiles,
batch_parser_script,
......@@ -183,7 +183,7 @@ workflow {
if( params.enable_codex )
SUB_CNV_CODEX (
SUB_BAM_FILTERING.out,
SUB_BAM_FILTERING.out.collect(),
samples,
bed,
params.codex_max_len
......
process MANTA {
tag "manta"
tag { "manta" }
container 'quay.io/biocontainers/manta:1.6.0--py27_0'
input:
......@@ -15,8 +15,12 @@ process MANTA {
script:
def exomeArgument = params.manta_exome ? "--exome" : ""
"""
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
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
cp generated\$(echo \$srr)/results/variants/diploidSV.vcf.gz ./\$(echo \$srr).manta.raw.vcf.gz
done
"""
}
\ No newline at end of file
process MANTA_FILTER {
tag "manta filter"
tag { "manta filter" }
input:
path script
......
process SVTOOLS {
tag "svtools"
tag { "svtools" }
container 'quay.io/biocontainers/svtools:0.5.1--py_0'
input:
......
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