Add initial IGV_HaplotypeViz WDL workflow for generating IGV screenshots

wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz.wdl

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+version 1.0
+
+workflow IGVScreenshotWorkflow {
+
+    input {
+        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
+        String sample_name
+        Int image_height = 500
+        Int memory_mb = 4000
+        Int disk_gb = 100           # Disk size in GB, default to 100 GB
+        String docker_image = "us.gcr.io/broad-dsp-lrma/igv_screenshot_docker:v982024"  # The Docker image to use
+    }
+
+    call RunIGVScreenshot {
+        input:
+            aligned_bam_hap1 = aligned_bam_hap1,
+            aligned_bam_hap1_bai = aligned_bam_hap1_bai,
+            aligned_bam_hap2 = aligned_bam_hap2,
+            aligned_bam_hap2_bai = aligned_bam_hap2_bai,
+            alignments = alignments,
+            alignments_bai = alignments_bai,
+            bed_file = bed_file,
+            fasta_file = fasta_file,
+            fasta_file_fai = fasta_file_fai,
+            sample_name = sample_name,
+            image_height = image_height,
+            memory_mb = memory_mb,
+            disk_gb = disk_gb,
+            docker_image = docker_image
+    }
+
+    output {
+        Array[File] snapshots = RunIGVScreenshot.snapshots
+    }
+}
+
+task RunIGVScreenshot {
+
+    input {
+        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
+        String sample_name
+        Int image_height
+        Int memory_mb
+        Int disk_gb
+        String docker_image
+    }
+
+    command <<<
+        set -euo pipefail
+
+        # Ensure the snapshots directory exists
+        mkdir -p '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} \
+          -r ~{bed_file} \
+          -ht ~{image_height} \
+          -bin /opt/IGV_Linux_2.18.2/igv.sh \
+          -mem ~{memory_mb} \
+          --fasta_file ~{fasta_file} \
+          --sample_name ~{sample_name}
+
+        # Move the screenshots to the IGV_Snapshots directory
+        #mv -- *.png 'output/IGV_Snapshots/'
+    >>>
+
+    runtime {
+        docker: docker_image
+        memory: "~{memory_mb} MB"
+        cpu: 2
+        disks: "local-disk ~{disk_gb} SSD"
+    }
+
+    output {
+        Array[File] snapshots = glob("output/IGV_Snapshots/*.png")
+    }
+}

wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz_bai_try.wdl

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+version 1.0
+
+workflow IGVScreenshotWorkflow {
+
+    input {
+        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
+        String docker_image = "us.gcr.io/broad-dsp-lrma/igv_screenshot_docker:v982024"  # The Docker image to use
+    }
+
+    call RunIGVScreenshot {
+        input:
+            aligned_bam_hap1 = aligned_bam_hap1,
+            aligned_bam_hap1_bai = aligned_bam_hap1_bai,
+            aligned_bam_hap2 = aligned_bam_hap2,
+            aligned_bam_hap2_bai = aligned_bam_hap2_bai,
+            alignments = alignments,
+            alignments_bai = alignments_bai,
+            bed_file = bed_file,
+            fasta_file = fasta_file,
+            fasta_file_fai = fasta_file_fai,
+            sample_name = sample_name,
+            image_height = image_height,
+            memory_mb = memory_mb,
+            disk_gb = disk_gb,
+            docker_image = docker_image
+    }
+
+    output {
+        Array[File] snapshots = RunIGVScreenshot.snapshots
+    }
+}
+
+task RunIGVScreenshot {
+
+    input {
+        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
+        String sample_name
+        Int image_height
+        Int memory_mb
+        Int disk_gb
+        String docker_image
+    }
+
+    command <<<
+        set -euo pipefail
+
+        # Ensure the snapshots directory exists under the mounted disk path
+        mkdir -p 'output/IGV_Snapshots/'
+        #mkdir snap_out
+
+        # 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, no --snapshot-dir
+        python3 /opt/IGV_Linux_2.18.2/make_igv_screenshot.py \
+          ~{aligned_bam_hap1} ~{aligned_bam_hap2} ~{alignments} \
+          -r ~{bed_file} \
+          -ht ~{image_height} \
+          -bin /opt/IGV_Linux_2.18.2/igv.sh \
+          -mem ~{memory_mb} \
+          --fasta_file ~{fasta_file} \
+          --sample_name ~{sample_name}
+
+        # Move the screenshots to the output directory
+        # mv -- *.png 'output/IGV_Snapshots/'
+    >>>
+
+    runtime {
+        docker: docker_image
+        memory: "~{memory_mb} MB"
+        cpu: 2
+        disks: "local-disk ~{disk_gb} SSD"
+    }
+
+    output {
+        Array[File] snapshots = glob("output/IGV_Snapshots/*.png")
+    }
+}