coerce aligned_bam? to aligned_bam

tomkinsc · tomkinsc · commit 8164dee2b0bf · 2025-02-28T16:41:32.000-05:00
coerce aligned_bam? to aligned_bam, which may fail at runtime but it shouldn't matter here
diff --git a/pipes/WDL/workflows/genbank_single.wdl b/pipes/WDL/workflows/genbank_single.wdl
@@ -137,7 +137,7 @@ workflow genbank_single {
         call ncbi.structured_comments_from_aligned_bam {
           input:
             out_basename = assembly_id,
-            aligned_bam = aligned_bam
+            aligned_bam = select_first([aligned_bam])
         }
     }
 

Original file line number	Diff line number	Diff line change
`@@ -137,7 +137,7 @@ workflow genbank_single {`
`137`	`137`	`call ncbi.structured_comments_from_aligned_bam {`
`138`	`138`	`input:`
`139`	`139`	`out_basename = assembly_id,`
`140`		`- aligned_bam = aligned_bam`
	`140`	`+ aligned_bam = select_first([aligned_bam])`
`141`	`141`	`}`
`142`	`142`	`}`
`143`	`143`