Merge pull request #319 from wtsi-npg/devel

merge devel branch to master branch (release 0.36.0 prep)
wtsi-npg · Jun 8, 2023 · 0f3279d · 0f3279d
2 parents 9532be5 + 0aef086
commit 0f3279d
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diff --git a/Changes b/Changes
@@ -1,6 +1,8 @@
 CHANGES LOG
 -----------
 
+ - add hs_bwa_executable  parameter to allow different bwa executables for target and nchs alignments (e.g. bwa-mem2 and bwa0_6)
+
 0.35.0
  - replace scramble with samtools in analysis pipeline templates
 

diff --git a/data/vtlib/markdup_biobambam.json b/data/vtlib/markdup_biobambam.json
@@ -46,6 +46,7 @@
 			{"subst":"bmd_metrics_file_flag"},
 			{"subst":"bmd_resetdupflag"},
 			{"subst":"bsmd_maxreadlen_flag","required":false,"ifnull":{"subst_constructor":{"vals":[ "maxreadlen", {"subst":"bsmd_maxreadlen_val","required":true, "ifnull":"500"} ],"postproc":{"op":"concat","pad":"="}}}},
+                        {"subst":"optical_distance_flag","ifnull":{"subst_constructor":{"vals":[ "optminpixeldif", {"subst":"markdup_optical_distance_value","required":false,"ifnull":2500} ], "postproc":{"op":"concat","pad":"="}}}},
 			{"subst":"bsmd_arbitrary_flags"}
 		]
 	}

diff --git a/data/vtlib/target_nchs_alignment.json b/data/vtlib/target_nchs_alignment.json
@@ -187,6 +187,9 @@
 		"type":"VTFILE",
 		"comment":"inputs: _stdin_ (bam), reference; outputs: _stdout_ (bam)",
 		"node_prefix":"alntgt_hs_",
+                "subst_map":{
+			"bwa_executable":{"subst":"hs_bwa_executable", "ifnull":{"subst":"bwa_executable"}}
+		},
 		"orig_name":{"subst":"alignment_vtf"},
 		"name":{
 			"subst":"alignment_vtf",