Commit e79224f4 authored by amunoz's avatar amunoz Committed by lrodrin
Browse files

minor changes in main.nf and modules/gridss.nf

parent e6f71ceb
......@@ -72,6 +72,7 @@ params.bits_set = 4
params.algoType = ''
params.assemblyFilename = "gridss.assembly.bam"
params.read_group = "@RG\\tID:SRR709972\\tSM:NA19206\\tPL:ILLUMINA\\tCN:CBRA\\tLB:Fragment"
params.manta_exome = true
/*
* Include subworkflows
......@@ -140,22 +141,23 @@ workflow {
if( params.enable_manta )
SUB_CNV_MANTA (
SUB_BAM_FILTERING.out.collect(),
SUB_BAM_FILTERING.out.collect().toSortedList(),
samples,
reference_fasta,
indexFiles,
bed,
tbi,
params.manta_exome,
manta_filter_script,
collapse_script,
tbi,
params.manta_max_len,
params.manta_min_len,
params.manta_min_q
)
if( params.enable_gridss )
SUB_CNV_GRIDSS (
SUB_BAM_FILTERING.out.collect(),
SUB_BAM_FILTERING.out.collect().toSortedList(),
samples,
reference_fasta,
indexFiles,
......@@ -170,7 +172,7 @@ workflow {
if( params.enable_exomeDepth )
SUB_CNV_EXOMEDEPTH (
SUB_BAM_FILTERING.out.collect(),
SUB_BAM_FILTERING.out.collect().toSortedList(),
samples,
indexFiles,
batch_parser_script,
......@@ -184,7 +186,7 @@ workflow {
if( params.enable_codex )
SUB_CNV_CODEX (
SUB_BAM_FILTERING.out.collect(),
SUB_BAM_FILTERING.out.collect().toSortedList(),
samples,
bed,
params.codex_max_len
......@@ -193,4 +195,4 @@ workflow {
)
SUB_FINAL_FILTERING(final_filtering)
}
}
\ No newline at end of file
......@@ -3,18 +3,18 @@ process GRIDSS {
container 'quay.io/biocontainers/gridss:2.9.3--0'
input:
tuple path(input), path(bai)
tuple path(bams), path(bais)
path reference_genome
path indexs
path blacklist
output:
path "*.gridss.raw.vcf.gz", emit: output
path "*.gridss.raw.vcf.gz"
script:
def threadsArgument = params.threads_gridss ? "--threads $params.threads_gridss" : ""
"""
for i in $input
for i in $bams
do
srr=\$(echo \$i | cut -f 1 -d '.')
......
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