Cram support

definitions/pipelines/rnaseq.cwl

@@ -9,12 +9,15 @@ requirements:
     - class: ScatterFeatureRequirement
     - class: InlineJavascriptRequirement
 inputs:
+    cram_reference:
+        type: File?
+        doc: Reference file used for cram decompression
     reference_index:
         type: File #this requires an extra file with the basename
         secondaryFiles: [".1.ht2", ".2.ht2", ".3.ht2", ".4.ht2", ".5.ht2", ".6.ht2", ".7.ht2", ".8.ht2"]
     reference_annotation:
         type: File
-    instrument_data_bams:
+    instrument_data:
         type: File[]
     read_group_id:
         type: string[]
@@ -76,12 +79,13 @@ outputs:
         type: File
         outputSource: kallisto/fusion_evidence
 steps:
-    bam_to_trimmed_fastq_and_hisat_alignments:
-        run: ../subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl
-        scatter: [bam, read_group_id, read_group_fields]
+    input_to_trimmed_fastq_and_hisat_alignments:
+        run: ../subworkflows/input_to_trimmed_fastq_and_hisat_alignments.cwl
+        scatter: [input, read_group_id, read_group_fields]
         scatterMethod: dotproduct
         in:
-            bam: instrument_data_bams
+            cram_reference: cram_reference
+            input: instrument_data
             read_group_id: read_group_id
             read_group_fields: read_group_fields
             adapters: trimming_adapters
@@ -99,7 +103,7 @@ steps:
             kallisto_index: kallisto_index
             strand: strand
             fastqs:
-                source: bam_to_trimmed_fastq_and_hisat_alignments/fastqs
+                source: input_to_trimmed_fastq_and_hisat_alignments/fastqs
                 valueFrom: |
                     ${
                       for(var i=0;i<self.length;i++){self[i] = self[i].reverse()}
@@ -117,7 +121,7 @@ steps:
     merge:
         run: ../tools/merge_bams.cwl
         in:
-            bams: bam_to_trimmed_fastq_and_hisat_alignments/aligned_bam
+            bams: input_to_trimmed_fastq_and_hisat_alignments/aligned_bam
         out:
             [merged_bam]
     index_bam:

definitions/subworkflows/bam_to_trimmed_fastq_and_hisat_alignments.cwl → definitions/subworkflows/input_to_trimmed_fastq_and_hisat_alignments.cwl

@@ -8,7 +8,9 @@ requirements:
     - class: SubworkflowFeatureRequirement
     - class: InlineJavascriptRequirement
 inputs:
-    bam:
+    cram_reference:
+        type: File?
+    input:
         type: File
     adapters:
         type: File
@@ -39,10 +41,21 @@ outputs:
         type: File
         outputSource: hisat2_align/aligned_bam
 steps:
+    input_to_bam:
+        run: ../tools/input_to_bam.cwl
+        in:
+            input: input
+            cram_reference: cram_reference
+        out: [bam_file]
+    revert_bam:
+        run: ../tools/revert_input.cwl
+        in:
+            bam: input_to_bam/bam_file
+        out: [reverted_bam]
     bam_to_fastq:
         run: ../tools/bam_to_fastq.cwl
         in:
-            bam: bam
+            bam: revert_bam/reverted_bam
         out:
             [fastq1, fastq2]
     trim_fastq:
@@ -61,10 +74,10 @@ steps:
         run: ../tools/hisat2_align.cwl
         in:
             reference_index: reference_index
-            fastq1: 
+            fastq1:
                 source: trim_fastq/fastqs
                 valueFrom: $(self[0])
-            fastq2: 
+            fastq2:
                 source: trim_fastq/fastqs
                 valueFrom: $(self[1])
             read_group_id: read_group_id

definitions/tools/input_to_bam.cwl

@@ -0,0 +1,42 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+
+cwlVersion: v1.0
+
+baseCommand: [ "samtools", "view" ]
+
+requirements:
+  - class: DockerRequirement
+    dockerImageId: zlskidmore/samtools:1.9
+    dockerPull: zlskidmore/samtools:1.9
+  - class: ResourceRequirement
+    ramMin: 20000
+    coresMin: 8
+
+arguments:
+  - valueFrom: "8"
+    position: 1
+    prefix: "--threads"
+  - valueFrom: "file.bam"
+    position: 2
+    prefix: "-o"
+  - valueFrom: "-b"
+    position: 3
+
+inputs:
+  input:
+    type: File
+    inputBinding:
+      position: 5
+  cram_reference:
+    type: File?
+    inputBinding:
+      position: 4
+      prefix: "-T"
+
+outputs:
+  bam_file:
+    type: File
+    outputBinding:
+      glob: file.bam

definitions/tools/revert_input.cwl

@@ -0,0 +1,30 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+label: "Picard: Revert Input"
+baseCommand: ["/usr/bin/java", "-Xmx4g", "-jar", "/opt/picard/picard.jar", "RevertSam", "VALIDATION_STRINGENCY=SILENT"]
+requirements:
+    - class: ResourceRequirement
+      coresMin: 1
+      ramMin: 6000
+      tmpdirMin: 25000
+    - class: DockerRequirement
+      dockerPull: "mgibio/rnaseq"
+arguments:
+    - valueFrom: "reverted.bam"
+      position: 2
+      prefix: "O="
+
+inputs:
+    bam:
+        type: File
+        inputBinding:
+            prefix: "I="
+            separate: false
+            position: 1
+outputs:
+    reverted_bam:
+        type: File
+        outputBinding:
+            glob: "reverted.bam"

example_data/rnaseq/workflow.yaml

@@ -1,4 +1,4 @@
-instrument_data_bams:
+instrument_data:
     - class: File
       path: gerald_H3MYFBBXX_4_GCCAAT_1k.bam
     - class: File