set defaults for samtools import flags "-i" and "-T", and make them o…

…ptional
wtsi-npg · Aug 13, 2024 · ec6c748 · ec6c748
1 parent b0e1927
commit ec6c748
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/data/vtlib/fastq_s2_pi.json b/data/vtlib/fastq_s2_pi.json
@@ -45,7 +45,8 @@
 				"-R", {"subst":"fastq_s2_pi_RG_ID","required":true, "comment":"readgroup"},
 				"-1", {"subst":"fastq_s2_pi_fq1","required":true, "comment":"FASTQ read 1"},
 				"-2", {"subst":"fastq_s2_pi_fq2","required":true, "comment":"FASTQ read 2"},
-				"-i",
+				{"select":"parse_casava_id", "default":"on", "select_range":[1], "cases":{ "on":["-i"], "off":[] }},
+				{"subst":"parse_import_tags_flag", "ifnull":["-T", {"subst":"parse_import_tags","required":true,"ifnull":"*"}]},
 				"-u",
 				"-O", "bam"
 			]