fix strandedness value when strand unknown

eascarrunz · eascarrunz · commit 28349e659787 · 2025-06-23T14:13:14.000+02:00
diff --git a/modules/reditools2.nf b/modules/reditools2.nf
@@ -28,7 +28,7 @@ process reditools2 {
         // Unsupported: Pass the library type string so that it's reported in
         // the reditools error message
         print("invalid strand \"${meta.strandedness}\"")
-        strand_orientation = meta.strandedness
+        strand_orientation = 0
     }
     base_name = bam.BaseName
     
diff --git a/modules/reditools3.nf b/modules/reditools3.nf
@@ -27,7 +27,7 @@ process reditools3 {
             // Unsupported: Pass the library type string so that it's reported in
             // the reditools error message
             print("invalid strand ${meta.strandedness}")
-            strand_orientation = meta.strandedness
+            strand_orientation =0
         }
         base_name = bam.BaseName
 

Original file line number	Diff line number	Diff line change
`@@ -28,7 +28,7 @@ process reditools2 {`
`28`	`28`	`// Unsupported: Pass the library type string so that it's reported in`
`29`	`29`	`// the reditools error message`
`30`	`30`	`print("invalid strand \"${meta.strandedness}\"")`
`31`		`- strand_orientation = meta.strandedness`
	`31`	`+ strand_orientation = 0`
`32`	`32`	`}`
`33`	`33`	`base_name = bam.BaseName`
`34`	`34`
Original file line number	Diff line number	Diff line change
`@@ -27,7 +27,7 @@ process reditools3 {`
`27`	`27`	`// Unsupported: Pass the library type string so that it's reported in`
`28`	`28`	`// the reditools error message`
`29`	`29`	`print("invalid strand ${meta.strandedness}")`
`30`		`- strand_orientation = meta.strandedness`
	`30`	`+ strand_orientation =0`
`31`	`31`	`}`
`32`	`32`	`base_name = bam.BaseName`
`33`	`33`