Commit 0ae880d7 authored by Acivico's avatar Acivico
Browse files

Minor changes in the cnv's

parent 08ca4872
......@@ -138,30 +138,57 @@ workflow {
SUB_PICARD_MARKDUPLICATES.out.alignments
)
SUB_CNV_MANTA (
if( params.enable_manta )
SUB_CNV_MANTA (
SUB_BAM_FILTERING.out,
samples,
indexFiles,
bed
)
SUB_CNV_GRIDSS (
SUB_BAM_FILTERING.out,
samples,
indexFiles
)
SUB_CNV_EXOMEDEPTH (
bed,
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,
samples,
indexFiles
)
SUB_CNV_CODEX(
SUB_BAM_FILTERING.out,
samples,
bed
)
indexFiles,
blacklist,
structural_variants_script,
gridss_filter_script,
collapse_script,
params.gridss_max_len,
params.gridss_min_len,
params.gridss_min_q
)
if( params.enable_exomeDepth )
SUB_CNV_EXOMEDEPTH (
SUB_BAM_FILTERING.out,
samples,
indexFiles,
batch_parser_script,
exomeDepth_script,
exomedepth_filter_script,
collapse_script,
params.exomedepth_min_len,
params.exomedepth_max_len,
params.exomedepth_min_bf
)
if( params.enable_codex )
SUB_CNV_CODEX (
SUB_BAM_FILTERING.out,
samples,
bed,
params.codex_max_len
params.codex_min_len
params.codex_min_lratio
)
SUB_FINAL_FILTERING(final_filtering)
}
......@@ -5,12 +5,15 @@ process CODEX_FILTER {
path input
path sample
path script
val max_len
val min_len
val min_lratio
output:
path "*.bed", emit: output
script:
"""
bash -c $script $input $samples $params.codex_min_len $params.codex_max_len $params.codex_min_lratio
sh $script $input $samples $min_len $max_len $min_lratio
"""
}
\ No newline at end of file
......@@ -5,12 +5,15 @@ process EXOMEDEPTH_FILTER {
path script
path input
path samples
val max_len
val min_len
val min_bf
output:
path "*.bed", emit: output
script:
"""
bash -c $script $input $sample $params.exomedepth_min_len $params.exomedepth_max_len $params.exomedepth_min_bf
sh $script $input $sample $min_len $max_len $min_bf
"""
}
\ No newline at end of file
......@@ -5,12 +5,15 @@ process GRIDSS_FILTER {
path script
path input
path sample
val max_len
val min_len
val min_q
output:
path "*", emit: output
script:
"""
sh $script $input $sample $params.gridss_min_len $params.gridss_max_len $params.gridss_min_q
sh $script $input $sample $min_len $max_len $min_q
"""
}
......@@ -5,6 +5,9 @@ process MANTA_FILTER {
path script
path input
path sample
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 $sample $min_len $max_len $min_q
done
"""
}
\ No newline at end of file
......@@ -22,11 +22,13 @@ workflow SUB_CNV_CODEX {
bams
samples
bed
max_len
min_len
min_lratio
main:
BATCH_PARSER( bams, samples, batch_parser_script )
CODEX( bams, BATCH_PARSER.out, bed, codex_script)
CODEX_FILTER( CODEX.out, samples, codex_filter_script )
CODEX_FILTER( CODEX.out, samples, codex_filter_script, max_len, min_len, min_lratio )
CODEX_UNION( CODEX_FILTER.out )
CODEX_MERGE( collapse_script, CODEX_UNION.out )
......
......@@ -25,11 +25,14 @@ workflow SUB_CNV_EXOMEDEPTH {
bams
samples
reference_genome
max_len
min_len
min_bf
main:
BATCH_PARSER( bams, samples, batch_parser_script )
EXOME_DEPTH( bams, BATCH_PARSER.out, reference_genome, exomeDepth_script )
EXOMEDEPTH_FILTER( exomedepth_filter_script, EXOME_DEPTH.out, samples )
EXOMEDEPTH_FILTER( exomedepth_filter_script, EXOME_DEPTH.out, samples, max_len, min_len, min_bf )
EXOMEDEPTH_UNION( EXOMEDEPTH_FILTER.out )
EXOMEDEPTH_MERGE( collapse_script, EXOMEDEPTH_UNION.out )
......
......@@ -26,13 +26,16 @@ workflow SUB_CNV_GRIDSS {
bams
samples
reference_genome
max_len
min_len
min_q
main:
GRIDSS(bams,
reference_genome,
blacklist)
STRUCTURAL_VARIANTS( GRIDSS.out, structural_variants_script )
GRIDSS_FILTER( gridss_filter_script, STRUCTURAL_VARIANTS.out, samples )
GRIDSS_FILTER( gridss_filter_script, STRUCTURAL_VARIANTS.out, samples, max_len, min_len, min_q )
GRIDSS_UNION( GRIDSS_FILTER.out )
GRIDSS_MERGE( collapse_script, GRIDSS_UNION.out )
......
......@@ -27,13 +27,16 @@ workflow SUB_CNV_MANTA {
samples
reference_genome
bed
max_len
min_len
min_q
main:
MANTA(bams,
reference_genome,
bed)
SVTOOLS( MANTA.out )
MANTA_FILTER( manta_filter_script, SVTOOLS.out, samples )
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 )
......
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