Commit 0ee8e6c6 authored by lrodrig1's avatar lrodrig1
Browse files

passing params from main to modules in manta subworkflow

parent bbfbc553
......@@ -3,18 +3,20 @@ process MANTA {
container 'quay.io/biocontainers/manta:1.6.0--py27_0'
input:
tuple path(bams), path(bais)
// tuple path(bams), path(bais)
path bams
path bais
path reference_genome
path indexs
path bed
path bed_tbi
val manta_exome
val exome
output:
tuple path("*.manta.raw.vcf.gz"), emit: output
script:
def exomeArgument = manta_exome ? "--exome" : ""
def exomeArgument = exome ? "--exome" : ""
"""
for i in $bams
do
......
process MANTA_FILTER {
tag "manta filter"
tag { "manta filter" }
input:
path script
path input
path sample
path samples
val max_len
val min_len
val min_q
output:
path "*", emit: output
......@@ -13,7 +16,7 @@ process MANTA_FILTER {
"""
for i in $input
do
sh $script \$i $sample $params.manta_min_len $params.manta_max_len $params.manta_min_q
sh $script \$i $samples $min_len $max_len $min_q
done
"""
}
\ No newline at end of file
}
/*
/*
* Include for cnv_manta
*/
include {
......@@ -24,19 +24,27 @@ include {
workflow SUB_CNV_MANTA {
take:
bams
bais
samples
reference_genome
indexs
bed
bed_tbi
exome
manta_filter_script
collapse_script
max_len
min_len
min_q
main:
MANTA(bams,
reference_genome,
bed)
SVTOOLS( MANTA.out )
MANTA_FILTER( manta_filter_script, SVTOOLS.out, samples )
MANTA_UNION( MANTA_FILTER.out )
MANTA_MERGE( collapse_script, MANTA_UNION.out )
MANTA(bams, bais, reference_genome, indexs, bed, bed_tbi, exome)
SVTOOLS(MANTA.out)
MANTA_FILTER(manta_filter_script, SVTOOLS.out, samples, max_len, min_len, min_q)
MANTA_UNION(MANTA_FILTER.out)
MANTA_MERGE(collapse_script, MANTA_UNION.out)
emit:
output = MANTA_MERGE.out
}
\ No newline at end of file
output = MANTA_MERGE.out
}
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment