From 779215397d1ae69870dfce47a59cf3694336d59a Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Tue, 20 Aug 2024 15:41:25 -0400 Subject: [PATCH] update modules.config --- conf/modules.config | 42 +++++++++++++++++++++++++++++++++++++++--- 1 file changed, 39 insertions(+), 3 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 33e9f467..ff0a212e 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -130,7 +130,16 @@ process { ] } - withName: 'PRESTO_MASKPRIMERS_SCORE_UMI_*' { + withName: 'PRESTO_MASKPRIMERS_SCORE_UMI_R1' { + publishDir = [ + path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args2 = "-f ID PRIMER ERROR" + } + + withName: 'PRESTO_MASKPRIMERS_SCORE_UMI_R2' { publishDir = [ path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, mode: params.publish_dir_mode, @@ -159,7 +168,16 @@ process { ext.args2 = '-f ID PRIMER ERROR --outname cregion_alignment' } - withName: 'PRESTO_MASKPRIMERS_EXTRACT*' { + withName: 'PRESTO_MASKPRIMERS_EXTRACT' { + publishDir = [ + path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args2 = '-f ID PRIMER ERROR PRSTART' + } + + withName: 'PRESTO_MASKPRIMERS_EXTRACT_R1' { publishDir = [ path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, mode: params.publish_dir_mode, @@ -168,7 +186,25 @@ process { ext.args2 = '-f ID PRIMER ERROR PRSTART' } - withName: 'PRESTO_MASKPRIMERS_SCORE_SANSUMI*' { + withName: 'PRESTO_MASKPRIMERS_EXTRACT_R2' { + publishDir = [ + path: { "${params.outdir}/presto/02-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args2 = '-f ID PRIMER ERROR PRSTART' + } + + withName: 'PRESTO_MASKPRIMERS_SCORE_SANSUMI_FWD' { + publishDir = [ + path: { "${params.outdir}/presto/03-maskprimers/${meta.id}" }, + mode: params.publish_dir_mode, + pattern: "*{txt,log,tab}" + ] + ext.args2 = '-f ID PRIMER ERROR' + } + + withName: 'PRESTO_MASKPRIMERS_SCORE_SANSUMI_REV' { publishDir = [ path: { "${params.outdir}/presto/03-maskprimers/${meta.id}" }, mode: params.publish_dir_mode,