From ad05e6d0acd0cf992814608a630d5f684004c38d Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Tue, 3 Oct 2023 12:10:45 +0100 Subject: [PATCH] add primer_clip_unmap_len_flag (default to no flag) and primer_clip_arbitrary_flags to samtools ampliconclip command in markdup_none --- data/vtlib/markdup_none.json | 2 ++ 1 file changed, 2 insertions(+) diff --git a/data/vtlib/markdup_none.json b/data/vtlib/markdup_none.json index f279a3701..c4c25c12a 100644 --- a/data/vtlib/markdup_none.json +++ b/data/vtlib/markdup_none.json @@ -20,7 +20,9 @@ {"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "ampliconclip", "-@", {"subst":"primer_clip_threads","required":true,"ifnull":4}, "-b", {"subst":"primer_clip_bed","required":true,"ifnull":"/nfs/srpipe_references/primer_panel/nCoV-2019/V2/SARS-CoV-2/MN908947.3/nCoV-2019.bed"}, + {"subst":"primer_clip_unmap_len_flag","ifnull":{"subst_constructor":{"vals":["--unmap-len", {"subst":"primer_clip_unmap_len_val","required":false}]}}}, {"select":"primer_clip_type", "required":true, "select_range":[1], "default":"unspecified", "cases":{"hard":"--hard-clip","soft":"--soft-clip","unspecified":[]}}, + {"subst":"primer_clip_arbitrary_flags"}, "-" ], "no_clip": [