change final_output_prep template to produce crai files using "samtoo…

…ls index" rather than "cram_index"
wtsi-npg · Nov 9, 2023 · bf05618 · bf05618
1 parent 6f748fc
commit bf05618
Showing 1 changed file with 8 additions and 2 deletions.
diff --git a/data/vtlib/final_output_prep.json b/data/vtlib/final_output_prep.json
@@ -368,7 +368,12 @@
 		"type":"EXEC",
 		"use_STDIN": true,
 		"use_STDOUT": false,
-		"cmd":[ "cram_index", "-", {"subst":"crai_file"} ]
+		"cmd": [
+			{"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "index",
+			{"subst":"cram_index_extra_flags", "required":false},
+			{"port":"cram", "direction":"in"},
+			{"port":"idx", "direction":"out"}
+		]
 	},
 	{
 		"id":"cram_seqchksum",
@@ -517,7 +522,8 @@
 		}
 	},
 	{ "id":"cram_tee_to_md5", "from":"cram_tee:md5", "to":"create_cram_md5" },
-	{ "id":"cram_tee_to_crai", "from":"cram_tee:crai", "to":"cram_index" },
+	{ "id":"bam_to_idx", "from":"cram_tee:crai", "to":"cram_index:cram" },
+	{ "id":"idx_to_file", "from":"cram_index:idx", "to":"crai_file" },
 	{ "id":"cram_tee_to_bscs", "from":"cram_tee:seqchksum", "to":"cram_seqchksum" },
 	{ "id":"md5_to_postprocess", "from":"create_cram_md5", "to":"postprocess_md5" },
 	{ "id":"bmdmw_to_sts_F0x900", "from":"bmd_multiway:samtools_stats_F0x900", "to":"samtools_stats_F0x900" },