Merge pull request #322 from wtsi-npg/devel

devel to master (release 0.37.0 prep)
wtsi-npg · Jul 25, 2023 · 6a00c5c · 6a00c5c
2 parents 5cd5eff + 67b666f
commit 6a00c5c
Showing 1 changed file with 8 additions and 0 deletions.
diff --git a/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json b/data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json
@@ -106,6 +106,14 @@
 				{"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":[]
+					}
+				},
 				{"subst":"i2b_arbitrary_flags", "comment":"this allows arbitrary sets of flag strings to be inserted in the command" },
 				"--output-file=-",
 				"--compression-level=0"