From 645b7f3b3a1e7eb49ff715cafc421dba8bd12a06 Mon Sep 17 00:00:00 2001 From: MarieLataretu Date: Wed, 3 Jan 2024 09:39:25 +0100 Subject: [PATCH 1/2] fix stub --- modules/alignment_processing.nf | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/modules/alignment_processing.nf b/modules/alignment_processing.nf index ca3b693..06bdc82 100644 --- a/modules/alignment_processing.nf +++ b/modules/alignment_processing.nf @@ -121,7 +121,7 @@ process filter_true_dcs_alignments { """ stub: """ - touch ${name}.no-dcs.bam ${name}.true-dcs.bam ${name}.false-dcs.bam ${name}.no-dcs.bam.bai ${name}.true-dcs.bam.bai ${name}.false-dcs.bam.bai + touch ${name}.no-dcs.bam ${name}.true-dcs.bam ${name}.false-dcs.bam ${name}.no-dcs.bam.bai ${name}.true-dcs.bam.bai ${name}.false-dcs.bam.bai dcs.bam dcs.bam.bai """ } @@ -154,6 +154,8 @@ process fastq_from_bam { fn.matches('.*.soft-clipped_merged.fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.soft-clipped_merged(.fast[aq].gz)$', '$1') : fn.matches('.*.unmapped_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') : fn.matches('.*.mapped_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') : + fn.matches('.*.unmapped_merged_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') : + fn.matches('.*.mapped_merged_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') : fn } ) From bfdc856efb2a368b820c519e848ad9c1cd22d915 Mon Sep 17 00:00:00 2001 From: MarieLataretu Date: Wed, 3 Jan 2024 09:47:47 +0100 Subject: [PATCH 2/2] publish (un)mapped_merged with keep --- modules/utils.nf | 2 ++ 1 file changed, 2 insertions(+) diff --git a/modules/utils.nf b/modules/utils.nf index 6b4e001..3a59335 100644 --- a/modules/utils.nf +++ b/modules/utils.nf @@ -108,6 +108,8 @@ process filter_fastq_by_name { fn.matches('.*.fast[aq].contamination.fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.fast[aq].contamination(.fast[aq].gz)$', '$1') : fn.matches('.*.unmapped_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') : fn.matches('.*.mapped_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') : + fn.matches('.*.unmapped_merged_(1|2|singleton).fast[aq].gz$') ? "clean/${fn}".replaceAll(~'.unmapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') : + fn.matches('.*.mapped_merged_(1|2|singleton).fast[aq].gz$') ? "removed/${fn}".replaceAll(~'.mapped_(1|2|singleton)(.fast[aq].gz)$', '_$1$2') : fn } )