From b2c08364fc9b092ea30d9a4f5409448266a3c916 Mon Sep 17 00:00:00 2001
From: Shadi Zaheri <szaheri@broadinstitute.org>
Date: Tue, 10 Sep 2024 17:05:35 -0400
Subject: [PATCH] fai

---
 wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz_bai_try.wdl | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz_bai_try.wdl b/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz_bai_try.wdl
index d9558132b..7490c60f0 100644
--- a/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz_bai_try.wdl
+++ b/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz_bai_try.wdl
@@ -11,6 +11,7 @@ workflow IGVScreenshotWorkflow {
         File alignments_bai         # BAM index for total alignments
         File bed_file               # BED file with regions
         File fasta_file             # Reference FASTA file
+        File fasta_fai              # FAI index for the FASTA file
         String sample_name          # Sample name to use in filenames
         Int image_height = 500
         Int memory_mb = 4000
@@ -28,6 +29,7 @@ workflow IGVScreenshotWorkflow {
             alignments_bai = alignments_bai,
             bed_file = bed_file,
             fasta_file = fasta_file,
+            fasta_fai = fasta_fai,
             sample_name = sample_name,
             image_height = image_height,
             memory_mb = memory_mb,
@@ -50,6 +52,7 @@ task RunIGVScreenshot {
         File alignments_bai
         File bed_file
         File fasta_file
+        File fasta_fai    # FAI index for the FASTA file
         String sample_name
         Int image_height
         Int memory_mb
@@ -71,6 +74,7 @@ task RunIGVScreenshot {
           -bin /opt/IGV_Linux_2.18.2/igv.sh \
           -mem ~{memory_mb} \
           --fasta_file ~{fasta_file} \
+          --fasta_fai ~{fasta_fai} \
           --sample_name ~{sample_name}
     }