diff --git a/conf/bladder.config b/conf/bladder.config index 77e7c3df..81020f39 100644 --- a/conf/bladder.config +++ b/conf/bladder.config @@ -29,7 +29,7 @@ params { profileexons = true profileintrons = true - consensus_min_depth = 100 + consensus_min_depth = 500 } diff --git a/conf/modules.config b/conf/modules.config index 52916568..9edec7d7 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -340,11 +340,10 @@ process { } withName: 'SUBSET_MUTRATE' { - ext.filters = { [ '"TYPE" : "SNV"' ].join(',\t').trim() - } + ext.filters = '' ext.output_fmt = { ['"header": true', - '"columns": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "canonical_SYMBOL"]', - '"colnames": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "GENE"]' + '"columns": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "canonical_SYMBOL", "TYPE"]', + '"colnames": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "GENE", "TYPE"]' ].join(',\t').trim() } @@ -354,12 +353,11 @@ process { } withName: 'BBG_DEEPCSA:DEEPCSA:MUTRATEPROT:SUBSET_MUTRATE' { - ext.filters = { ['"TYPE" : "SNV"', - '"Protein_affecting": "protein_affecting"'].join(',\t').trim() + ext.filters = { ['"Protein_affecting": "protein_affecting"'].join(',\t').trim() } ext.output_fmt = { ['"header": true', - '"columns": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "canonical_SYMBOL"]', - '"colnames": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "GENE"]' + '"columns": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "canonical_SYMBOL", "TYPE"]', + '"colnames": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "GENE", "TYPE"]' ].join(',\t').trim() } @@ -369,12 +367,11 @@ process { } withName: '.*NONPROT:SUBSET_MUTRATE' { - ext.filters = { ['"TYPE" : "SNV"', - '"Protein_affecting": "not protein_affecting"'].join(',\t').trim() + ext.filters = { ['"Protein_affecting": "not protein_affecting"'].join(',\t').trim() } ext.output_fmt = { ['"header": true', - '"columns": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "canonical_SYMBOL"]', - '"colnames": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "GENE"]' + '"columns": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "canonical_SYMBOL", "TYPE"]', + '"colnames": ["SAMPLE_ID", "MUT_ID", "ALT_DEPTH", "GENE", "TYPE"]' ].join(',\t').trim() }