fix bai

broadinstitute · Sep 10, 2024 · 7ac3c54 · 7ac3c54
1 parent 0b70896
commit 7ac3c54
Showing 1 changed file with 3 additions and 6 deletions.
diff --git a/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz.wdl b/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz.wdl
@@ -4,11 +4,8 @@ workflow IGVScreenshotWorkflow {
 
     input {
         File aligned_bam_hap1       # BAM file for haplotype 1
-        File aligned_bam_hap1_bai   # BAM index for haplotype 1
         File aligned_bam_hap2       # BAM file for haplotype 2
-        File aligned_bam_hap2_bai   # BAM index for haplotype 2
         File alignments             # BAM file for total alignments
-        File alignments_bai         # BAM index for total alignments
         File bed_file               # BED file with regions
         File fasta_file             # Reference FASTA file
         String sample_name          # Sample name to use in filenames
@@ -21,11 +18,11 @@ workflow IGVScreenshotWorkflow {
     call RunIGVScreenshot {
         input:
             aligned_bam_hap1 = aligned_bam_hap1,
-            aligned_bam_hap1_bai = aligned_bam_hap1_bai,
+            aligned_bam_hap1_bai = aligned_bam_hap1 + ".bai",  # Automatically infer BAI location
             aligned_bam_hap2 = aligned_bam_hap2,
-            aligned_bam_hap2_bai = aligned_bam_hap2_bai,
+            aligned_bam_hap2_bai = aligned_bam_hap2 + ".bai",  # Automatically infer BAI location
             alignments = alignments,
-            alignments_bai = alignments_bai,
+            alignments_bai = alignments + ".bai",  # Automatically infer BAI location
             bed_file = bed_file,
             fasta_file = fasta_file,
             sample_name = sample_name,