Create CramToBam.wdl

CramToBam/CramToBam.wdl

@@ -0,0 +1,106 @@
+version 1.0
+
+workflow CramToBamWorkflow {
+    input {
+        File referenceFasta
+        File referenceFai
+        File referenceDict
+        File cram_file
+        String sample_id
+        String docker_image
+        String gatk_docker
+        String output_mode
+    }
+    call CramToBam {
+        input: 
+            referenceFasta = referenceFasta,
+            referenceFai = referenceFai,
+            referenceDict = referenceDict,
+            cram_file = cram_file,
+            sample_id = sample_id,
+            docker_image = docker_image
+    }
+
+    call ValidateBam {
+        input: 
+            bam_file = CramToBam.output_bam,
+            sample_id = sample_id,
+            output_mode = output_mode,
+            gatk_docker = gatk_docker
+    }
+
+    output {
+        File bam_file = CramToBam.output_bam
+        File bam_index_file = CramToBam.output_bam_index
+        File validation_output = ValidateBam.validation_output
+    }
+}
+
+
+    task CramToBam {
+        input {
+        File referenceFasta
+        File referenceFai
+        File referenceDict
+        File cram_file
+        String sample_id
+        String docker_image = "broadinstitute/genomes-in-the-cloud:2.3.1-1504795437"
+        Int? mem_size
+        Int? disk_size
+        Int? preemptible_attempts
+        }
+        command <<<
+            set -e
+            set -o pipefail
+
+            ln -vs ~{referenceFasta} reference.fasta
+            ln -vs ~{referenceFai} reference.fasta.fai
+            ln -vs ~{referenceDict} reference.dict
+
+            samtools view -h -T reference.fasta ~{cram_file} |
+            samtools view -b -o ~{sample_id}.bam -
+            samtools index -b ~{sample_id}.bam
+            mv ~{sample_id}.bam.bai ~{sample_id}.bai
+        >>>
+        output {
+            File output_bam = "~{sample_id}.bam"
+            File output_bam_index = "~{sample_id}.bai"
+        }
+        runtime {
+            docker: docker_image
+            memory: select_first([mem_size, 4]) + " GB"
+            disks: "local-disk " + select_first([disk_size, 200]) + " HDD"
+            preemptible: select_first([preemptible_attempts, 2])
+        }
+}
+
+
+    task ValidateBam {
+        input {
+        File bam_file
+        String sample_id
+        String gatk_docker = "broadinstitute/gatk:4.6.0.0"
+        String output_mode = "SUMMARY"
+        Int? mem_size
+        Int? disk_size
+        Int? preemptible_attempts
+        }
+        Int machine_mem_mb = select_first([mem_size, 7]) * 1000
+        Int command_mem_mb = machine_mem_mb - 1000
+        command <<<
+            gatk --java-options "-Xmx~{command_mem_mb}m" ValidateSamFile \
+                --INPUT ~{bam_file} \
+                --OUTPUT "~{sample_id}_validation_output.txt" \
+                --MODE ~{output_mode}
+        >>>
+        output {
+            File validation_output = "~{sample_id}_validation_output.txt"
+        }
+        runtime {
+            docker: gatk_docker
+            memory: select_first([mem_size, 4]) + " GB"
+            disks: "local-disk " + select_first([disk_size, 100]) + " HDD"
+            preemptible: select_first([preemptible_attempts, 2])
+        }
+
+}