updated the cmmand section

wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz_bai_try.wdl

@@ -1,18 +1,18 @@
 version 1.0
 
 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
-        File fasta_fai              # FAI index for the FASTA file
-        String sample_name          # Sample name to use in filenames
+        File aligned_bam_hap1
+        File aligned_bam_hap1_bai
+        File aligned_bam_hap2
+        File aligned_bam_hap2_bai
+        File alignments
+        File alignments_bai
+        File bed_file
+        File fasta_file
+        File fasta_file_fai   # Include the .fai file
+        String sample_name
         Int image_height = 500
         Int memory_mb = 4000
         Int disk_gb = 100           # Disk size in GB, default to 100 GB
@@ -29,7 +29,7 @@ workflow IGVScreenshotWorkflow {
             alignments_bai = alignments_bai,
             bed_file = bed_file,
             fasta_file = fasta_file,
-            fasta_fai = fasta_fai,
+            fasta_file_fai = fasta_file_fai,
             sample_name = sample_name,
             image_height = image_height,
             memory_mb = memory_mb,
@@ -43,6 +43,7 @@ workflow IGVScreenshotWorkflow {
 }
 
 task RunIGVScreenshot {
+
     input {
         File aligned_bam_hap1
         File aligned_bam_hap1_bai
@@ -52,31 +53,32 @@ task RunIGVScreenshot {
         File alignments_bai
         File bed_file
         File fasta_file
-        File fasta_fai    # FAI index for the FASTA file
+        File fasta_file_fai
         String sample_name
         Int image_height
         Int memory_mb
         Int disk_gb
         String docker_image
     }
 
-    command {
-        mkdir -p IGV_Snapshots
+    command <<<
+        # Ensure the snapshots directory exists
+        mkdir -p /output/IGV_Snapshots && chmod 777 /output/IGV_Snapshots
+
+        # Start a virtual frame buffer to allow IGV to render
         Xvfb :1 -screen 0 1024x768x16 &> xvfb.log &
         export DISPLAY=:1
 
         # Run the IGV screenshot script with the provided inputs
         python3 /opt/IGV_Linux_2.18.2/make_igv_screenshot.py \
           ~{aligned_bam_hap1} ~{aligned_bam_hap2} ~{alignments} \
-          ~{aligned_bam_hap1_bai} ~{aligned_bam_hap2_bai} ~{alignments_bai} \
           -r ~{bed_file} \
           -ht ~{image_height} \
           -bin /opt/IGV_Linux_2.18.2/igv.sh \
           -mem ~{memory_mb} \
           --fasta_file ~{fasta_file} \
-          --fasta_fai ~{fasta_fai} \
           --sample_name ~{sample_name}
-    }
+    >>>
 
     runtime {
         docker: docker_image
@@ -86,6 +88,6 @@ task RunIGVScreenshot {
     }
 
     output {
-        Array[File] snapshots = glob("IGV_Snapshots/*.png")
+        Array[File] snapshots = glob("/output/IGV_Snapshots/*.png")
     }
 }