technically the same script as IGV_HaplotypeViz but will locate the i…

…nput bai as well

wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz_bai_try.wdl

@@ -0,0 +1,74 @@
+version 1.0
+
+workflow igv_screenshot_workflow {
+  input {
+    File aligned_bam_hap1          # BAM file for haplotype 1
+    File aligned_bam_hap2          # BAM file for haplotype 2
+    File alignments_bam            # Total alignments BAM file
+    File ref_fasta                 # Reference FASTA file
+    File targeted_bed_file         # BED file with regions of interest
+    String sample_name             # Sample name for naming convention
+    Int image_height = 500         # Height of IGV track, default to 500
+    Int memory_mb = 4000           # Memory for IGV, default to 4000MB
+  }
+
+  call make_igv_screenshot {
+    input:
+      aligned_bam_hap1 = aligned_bam_hap1,
+      aligned_bam_hap2 = aligned_bam_hap2,
+      alignments_bam = alignments_bam,
+      ref_fasta = ref_fasta,
+      targeted_bed_file = targeted_bed_file,
+      sample_name = sample_name,
+      image_height = image_height,
+      memory_mb = memory_mb
+  }
+
+  output {
+    Array[File] pngs = make_igv_screenshot.pngs  # Collect all generated PNG files
+  }
+}
+
+task make_igv_screenshot {
+  input {
+    File aligned_bam_hap1          # BAM file for haplotype 1
+    File aligned_bam_hap2          # BAM file for haplotype 2
+    File alignments_bam            # Total alignments BAM file
+    File ref_fasta                 # Reference FASTA file
+    File targeted_bed_file         # BED file with regions of interest
+    String sample_name             # Sample name for naming convention
+    Int image_height               # Height of IGV track
+    Int memory_mb                  # Memory for IGV
+  }
+
+  command {
+    # Create output directory for snapshots
+    mkdir -p IGV_Snapshots
+
+    # Start a virtual framebuffer (Xvfb) to allow IGV to render without display
+    Xvfb :1 -screen 0 1024x768x16 &> xvfb.log &
+    export DISPLAY=:1
+
+    # Run the Python script to generate IGV screenshots
+    python3 /opt/IGV_Linux_2.18.2/make_igv_screenshot.py \
+      ~{aligned_bam_hap1} ~{aligned_bam_hap2} ~{alignments_bam} \
+      -r ~{targeted_bed_file} \
+      -ht ~{image_height} \
+      -bin /opt/IGV_Linux_2.18.2/igv.sh \
+      -mem ~{memory_mb} \
+      --fasta_file ~{ref_fasta} \
+      --sample_name ~{sample_name}
+  }
+
+  output {
+    # Capture all generated PNG snapshot files
+    Array[File] pngs = glob("IGV_Snapshots/*.png")
+  }
+
+  runtime {
+    docker: "us.gcr.io/broad-dsp-lrma/igv_screenshot_docker:v982024"
+    memory: "~{memory_mb} MB"
+    cpu: 2
+    disks: "local-disk 50 HDD"  # Specify disk size if needed
+  }
+}