From fd4743531acf60597720e0810c64fed6397bc1f0 Mon Sep 17 00:00:00 2001 From: Kevin Lewis Date: Thu, 31 Aug 2023 12:09:09 +0100 Subject: [PATCH] change bambi i2b command in stage1 analysis to use new boolean version of --nocall-quality flag --- data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json | 9 +-------- 1 file changed, 1 insertion(+), 8 deletions(-) diff --git a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json index 2f5ffdcb..52aa889c 100644 --- a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json +++ b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json @@ -106,14 +106,7 @@ {"subst":"i2b_final_1_flag","ifnull":{"subst_constructor":{"vals":[ "--final-cycle", {"subst":"i2b_final_1"} ],"postproc":{"op":"concat","pad":"="}}}}, {"subst":"i2b_thread_count_flag","ifnull":{"subst_constructor":{"vals":[ "--threads", {"subst":"i2b_thread_count"} ],"postproc":{"op":"concat","pad":"="}}}}, {"subst":"i2b_tqlen_flag","ifnull":{"subst_constructor":{"vals":[ "--queue-len", {"subst":"i2b_tqlen"} ],"postproc":{"op":"concat","pad":"="}}}}, - {"select":"i2b_nocall_qual_switch", "required":true, "select_range":[1], "default":"off", - "cases":{ - "on": - {"subst":"i2b_nocall_qual_flag","ifnull":{"subst_constructor":{"vals":[ "--nocall-quality", {"subst":"i2b_nocall_qual", "ifnull":2} ],"postproc":{"op":"concat","pad":"="}}}}, - - "off":[] - } - }, + {"select":"i2b_nocall_qual_switch", "required":true, "select_range":[1], "default":"off", "cases":{ "on": "--nocall-quality", "off":[]}}, {"subst":"i2b_arbitrary_flags", "comment":"this allows arbitrary sets of flag strings to be inserted in the command" }, "--output-file=-", "--compression-level=0"