skip chrM in this new scheme

SHuang-Broad · SHuang-Broad · commit 71f6aad471f4 · 2025-04-01T00:23:55.000-04:00
diff --git a/wdl/deprecated/tasks/PEPPER-MARGIN-DeepVariant.wdl b/wdl/deprecated/tasks/PEPPER-MARGIN-DeepVariant.wdl
@@ -45,7 +45,7 @@ workflow Run {
     }
 
     scatter (triplet in how_to_shard_wg_for_calling) {
-        if (triplet.left != "alts") {
+        if (triplet.left != "alts" && triplet.left != "chrM") {
             call ONTPepper.Pepper {
                 input:
                     bam           = triplet.right.left,

Original file line number	Diff line number	Diff line change
`@@ -45,7 +45,7 @@ workflow Run {`
`45`	`45`	`}`
`46`	`46`
`47`	`47`	`scatter (triplet in how_to_shard_wg_for_calling) {`
`48`		`- if (triplet.left != "alts") {`
	`48`	`+ if (triplet.left != "alts" && triplet.left != "chrM") {`
`49`	`49`	`call ONTPepper.Pepper {`
`50`	`50`	`input:`
`51`	`51`	`bam = triplet.right.left,`