From bd53b9cce97594c29ac314d72e9f4a77ace081b1 Mon Sep 17 00:00:00 2001
From: Shadi Zaheri <szaheri@broadinstitute.org>
Date: Tue, 10 Sep 2024 13:16:51 -0400
Subject: [PATCH] new wdl-the script has been tested on the vm

---
 .../PacBio/Utility/IGV_HaplotypeViz.wdl       | 130 +++++++++---------
 1 file changed, 65 insertions(+), 65 deletions(-)

diff --git a/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz.wdl b/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz.wdl
index 1202411f3..6b3342843 100644
--- a/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz.wdl
+++ b/wdl/pipelines/PacBio/Utility/IGV_HaplotypeViz.wdl
@@ -1,77 +1,77 @@
 version 1.0
 
-workflow igv_screenshot_automation {
+workflow IGVScreenshotWorkflow {
 
-  input {
-    File asm_hap1_bam   # BAM file for asm haplotype 1
-    File asm_hap2_bam   # BAM file for asm haplotype 2
-    File bam            # A single BAM file for the sample
-    File reference_fasta  # Reference FASTA file
-    File regions_bed      # Path to the BED file with regions of interest
-    String genome         # Reference genome version (e.g., "hg38")
-    Int image_height = 500  # Height for the IGV tracks
-  }
+    input {
+        File aligned_bam_hap1       # BAM file for haplotype 1
+        File aligned_bam_hap2       # BAM file for haplotype 2
+        File alignments             # BAM file 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
+        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
+    }
 
-  # Directly use .bam.bai files co-located with the BAM files
-  call IGVScreenshotTask {
-    input:
-      asm_hap1_bam = asm_hap1_bam,
-      asm_hap1_bai = asm_hap1_bam + ".bai",
-      asm_hap2_bam = asm_hap2_bam,
-      asm_hap2_bai = asm_hap2_bam + ".bai",
-      bam = bam,
-      bam_bai = bam + ".bai",
-      reference_fasta = reference_fasta,
-      regions_bed = regions_bed,
-      genome = genome,
-      image_height = image_height
-  }
+    call RunIGVScreenshot {
+        input:
+            aligned_bam_hap1 = aligned_bam_hap1,
+            aligned_bam_hap2 = aligned_bam_hap2,
+            alignments = alignments,
+            bed_file = bed_file,
+            fasta_file = fasta_file,
+            sample_name = sample_name,
+            image_height = image_height,
+            memory_mb = memory_mb,
+            disk_gb = disk_gb,
+            docker_image = docker_image
+    }
 
-  output {
-    Array[File] snapshots = IGVScreenshotTask.snapshots
-  }
+    output {
+        Array[File] snapshots = RunIGVScreenshot.snapshots
+    }
 }
 
-task IGVScreenshotTask {
-  input {
-    File asm_hap1_bam
-    File asm_hap1_bai
-    File asm_hap2_bam
-    File asm_hap2_bai
-    File bam
-    File bam_bai
-    File reference_fasta
-    File regions_bed
-    String genome
-    Int image_height
-  }
+task RunIGVScreenshot {
+    input {
+        File aligned_bam_hap1
+        File aligned_bam_hap2
+        File alignments
+        File bed_file
+        File fasta_file
+        String sample_name
+        Int image_height
+        Int memory_mb
+        Int disk_gb
+        String docker_image
+    }
 
-  command {
-    # Localize the BAM and BAI files to ensure IGV can use them
-    ln -s ${asm_hap1_bam} .
-    ln -s ${asm_hap1_bai} .
-    ln -s ${asm_hap2_bam} .
-    ln -s ${asm_hap2_bai} .
-    ln -s ${bam} .
-    ln -s ${bam_bai} .
+    command {
+        mkdir -p IGV_Snapshots
+        Xvfb :1 -screen 0 1024x768x16 &> xvfb.log &
+        export DISPLAY=:1
 
-    # Run the Python script with inputs for asm_hap1, asm_hap2, and bam
-    python3 /opt/IGV_Linux_2.18.2/make_igv_screenshot.py \
-            ${asm_hap1_bam} ${asm_hap2_bam} ${bam} \
-            -r ${regions_bed} -g ${genome} -ht ${image_height} \
-            -ref_fasta ${reference_fasta} \
-            -bin /opt/IGV_Linux_2.18.2/igv.sh
-  }
+        # 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}
+    }
 
-  output {
-    # Capture all the snapshot files generated by the script from the 'IGV_Snapshots' directory
-    Array[File] snapshots = glob("IGV_Snapshots/*.png")
-  }
+    runtime {
+        docker: docker_image
+        memory: "~{memory_mb} MB"
+        cpu: 2
+        disks: "local-disk ~{disk_gb} HDD"
+    }
 
-  runtime {
-    docker: "us.gcr.io/broad-dsp-lrma/igv_screenshot_docker:v982024"
-    memory: "8G"
-    cpu: 2
-    disks: "local-disk 100 HDD"  # Adjust this based on file size needs
-  }
+    output {
+        Array[File] snapshots = glob("IGV_Snapshots/*.png")
+    }
 }