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