Merge pull request #325 from dozy/bambi_i2b_flag_tweak

change bambi i2b command (--nocall-quality)
wtsi-npg · Sep 7, 2023 · b06b444 · b06b444
2 parents 5f0c692 + fd47435
commit b06b444
Showing 1 changed file with 1 addition and 8 deletions.
diff --git 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"