From 2fbc095e599f5a383b1750c3a39788a9e6fb5364 Mon Sep 17 00:00:00 2001
From: Shadi Zaheri <szaheri@broadinstitute.org>
Date: Thu, 29 May 2025 16:26:43 -0400
Subject: [PATCH] Add CRAM to FASTQ WDL to resolve STAR alignment hang issues

---
 rnaseq/cram_ubam_fq.wdl | 171 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 171 insertions(+)
 create mode 100644 rnaseq/cram_ubam_fq.wdl

diff --git a/rnaseq/cram_ubam_fq.wdl b/rnaseq/cram_ubam_fq.wdl
new file mode 100644
index 0000000..fd31d95
--- /dev/null
+++ b/rnaseq/cram_ubam_fq.wdl
@@ -0,0 +1,171 @@
+version 1.0
+
+# CRAM to FASTQ Conversion Workflow
+# 
+# This workflow converts CRAM files back to FASTQ format through a three-step process:
+# 1. Convert CRAM to aligned BAM using samtools
+# 2. Revert aligned BAM to unmapped BAM (uBAM) using GATK RevertSam
+# 3. Extract paired-end and unpaired FASTQ files from uBAM using GATK SamToFastq
+#
+# The workflow outputs compressed FASTQ files (.fastq.gz) for:
+# - Read 1 (forward reads)
+# - Read 2 (reverse reads) 
+# - Unpaired reads (singletons)
+#
+# This is useful for re-processing sequencing data through different analysis pipelines
+# or when you need FASTQ files from archived CRAM data.
+
+workflow cram_to_fastq_workflow {
+  meta {
+    author: "Shadi Zaheri"
+    description: "Convert CRAM files to FASTQ format via BAM and uBAM intermediate steps"
+  }
+  input {
+    File cram_file
+    File reference_fasta
+    File reference_fasta_index
+    File reference_dict
+    String sample_id
+    String cram_to_bam_memory = "4G"
+    Int cram_to_bam_cpu = 2
+    String cram_to_bam_disk = "local-disk 20 HDD"
+    Int cram_to_bam_preemptible = 1
+
+    String bam_to_ubam_memory = "4G"
+    Int bam_to_ubam_cpu = 2
+    String bam_to_ubam_disk = "local-disk 20 HDD"
+    Int bam_to_ubam_preemptible = 1
+
+    String ubam_to_fastq_memory = "4G"
+    Int ubam_to_fastq_cpu = 2
+    String ubam_to_fastq_disk = "local-disk 20 HDD"
+    Int ubam_to_fastq_preemptible = 1
+  }
+
+  call CramToBam {
+    input:
+      cram = cram_file,
+      reference = reference_fasta,
+      memory = cram_to_bam_memory,
+      cpu = cram_to_bam_cpu,
+      disk = cram_to_bam_disk,
+      preemptible = cram_to_bam_preemptible
+  }
+
+  call BamToUbam {
+    input:
+      bam = CramToBam.bam,
+      reference = reference_fasta,
+      memory = bam_to_ubam_memory,
+      cpu = bam_to_ubam_cpu,
+      disk = bam_to_ubam_disk,
+      preemptible = bam_to_ubam_preemptible
+  }
+
+  call UbamToFastq {
+    input:
+      ubam = BamToUbam.ubam,
+      memory = ubam_to_fastq_memory,
+      cpu = ubam_to_fastq_cpu,
+      disk = ubam_to_fastq_disk,
+      preemptible = ubam_to_fastq_preemptible,
+      prefix = sample_id
+  }
+
+  output {
+    # Only compressed FASTQ outputs to match task outputs
+    File read1_fastq_gz = UbamToFastq.read1_fastq_gz
+    File read2_fastq_gz = UbamToFastq.read2_fastq_gz
+    File unpaired_fastq_gz = UbamToFastq.unpaired_fastq_gz
+  }
+}
+
+task CramToBam {
+  input {
+    File cram
+    File reference
+    String memory
+    Int cpu
+    String disk
+    Int preemptible
+  }
+  command {
+    samtools view -b -T ~{reference} ~{cram} > aligned.bam
+  }
+  output {
+    File bam = "aligned.bam"
+  }
+  runtime {
+    docker: "us.gcr.io/broad-gatk/gatk:latest"
+    memory: memory
+    cpu: cpu
+    disks: disk
+    preemptible: preemptible
+  }
+}
+
+task BamToUbam {
+  input {
+    File bam
+    File reference
+    String memory
+    Int cpu
+    String disk
+    Int preemptible
+  }
+  command {
+    gatk RevertSam \
+      -I ~{bam} \
+      -O unmapped.bam \
+      --SANITIZE true \
+      --REMOVE_ALIGNMENT_INFORMATION true \
+      --RESTORE_ORIGINAL_QUALITIES true
+  }
+  output {
+    File ubam = "unmapped.bam"
+  }
+  runtime {
+    docker: "us.gcr.io/broad-gatk/gatk:latest"
+    memory: memory
+    cpu: cpu
+    disks: disk
+    preemptible: preemptible
+  }
+}
+
+task UbamToFastq {
+  input {
+    File ubam
+    String prefix
+    String memory
+    Int cpu
+    String disk
+    Int preemptible
+  }
+  command {
+    gatk SamToFastq \
+      -I ~{ubam} \
+      -F ~{prefix}_1.fastq \
+      -F2 ~{prefix}_2.fastq \
+      -FU ~{prefix}_unpaired.fastq
+
+    gzip -c ~{prefix}_1.fastq > ~{prefix}_1.fastq.gz
+    gzip -c ~{prefix}_2.fastq > ~{prefix}_2.fastq.gz
+    gzip -c ~{prefix}_unpaired.fastq > ~{prefix}_unpaired.fastq.gz
+  }
+  output {
+    File read1_fastq_gz = "~{prefix}_1.fastq.gz"
+    File read2_fastq_gz = "~{prefix}_2.fastq.gz"
+    File unpaired_fastq_gz = "~{prefix}_unpaired.fastq.gz"
+  }
+  runtime {
+    docker: "us.gcr.io/broad-gatk/gatk:latest"
+    memory: memory
+    cpu: cpu
+    disks: disk
+    preemptible: preemptible
+  }
+  meta {
+    author: "Shadi Zaheri"
+  }
+}
\ No newline at end of file