Updating bisulfite pipeline to accept bams and fastqs

definitions/pipelines/bisulfite.cwl

@@ -7,27 +7,26 @@ requirements:
     - class: MultipleInputFeatureRequirement
     - class: SubworkflowFeatureRequirement
     - class: ScatterFeatureRequirement
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/sequence_data.yml
+          - $import: ../types/trimming_options.yml
 inputs:
     reference_index:
         type: string
     reference_sizes:
         type: File
-    instrument_data_bams:
-        type: File[]
-    read_group_id:
-        type: string[]
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
+        doc: |
+          sequence represents the sequencing data as either FASTQs or BAMs with accompanying
+          readgroup information. Note that in the @RG field ID and SM are required.
     sample_name:
         type: string
-    trimming_adapters:
-        type: File
-    trimming_adapter_trim_end:
-        type: string
-    trimming_adapter_min_overlap:
-        type: int
-    trimming_max_uncalled:
-        type: int
-    trimming_min_readlength:
-        type: int
+    trimming_options:
+        type:
+            - ../types/trimming_options.yml#trimming_options
+            - "null"
     QCannotation:
         type: File
     assay_non_cpg_sites:
@@ -54,39 +53,27 @@ outputs:
         type: Directory
         outputSource: bisulfite_qc/QC_directory
 steps:
-    bam_to_trimmed_fastq_and_biscuit_alignments:
-        run: ../subworkflows/bam_to_trimmed_fastq_and_biscuit_alignments.cwl
-        scatter: [bam, read_group_id]
-        scatterMethod: dotproduct
+    bisulfite_alignment:
+        run: ../subworkflows/sequence_to_bisulfite_alignment.cwl
         in:
-            bam: instrument_data_bams
-            read_group_id: read_group_id
-            adapters: trimming_adapters
-            adapter_trim_end: trimming_adapter_trim_end
-            adapter_min_overlap: trimming_adapter_min_overlap
-            max_uncalled: trimming_max_uncalled
-            min_readlength: trimming_min_readlength
+            sequence: sequence
+            trimming_options: trimming_options
             reference_index: reference_index
+            sample_name: sample_name
         out:
             [aligned_bam]
-    merge:
-        run: ../tools/merge_bams.cwl
-        in:
-            bams: bam_to_trimmed_fastq_and_biscuit_alignments/aligned_bam
-        out:
-            [merged_bam]
     pileup:
         run: ../tools/biscuit_pileup.cwl
         in:
-            bam: merge/merged_bam
+            bam: bisulfite_alignment/aligned_bam
             reference: reference_index
         out:
             [vcf]
     bisulfite_qc:
         run: ../subworkflows/bisulfite_qc.cwl
         in:
             vcf: pileup/vcf
-            bam: merge/merged_bam
+            bam: bisulfite_alignment/aligned_bam
             reference: reference_index
             QCannotation: QCannotation
         out:
@@ -110,7 +97,7 @@ steps:
         run: ../tools/bam_to_cram.cwl
         in:
             reference: reference_index
-            bam: merge/merged_bam
+            bam: bisulfite_alignment/aligned_bam
         out:
             [cram]
     index_cram:

definitions/subworkflows/sequence_to_bisulfite_alignment.cwl

@@ -0,0 +1,64 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "take bisulfite sequence data through trimming, alignment, and markdup"
+requirements:
+    - class: SubworkflowFeatureRequirement
+    - class: ScatterFeatureRequirement
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/sequence_data.yml
+          - $import: ../types/trimming_options.yml
+inputs:
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data[]
+        doc: "the unaligned sequence data with readgroup information"
+    trimming_options:
+        type:
+            - ../types/trimming_options.yml#trimming_options
+            - "null"
+    reference_index:
+        type: string
+    sample_name:
+        type: string
+outputs:
+    aligned_bam:
+        type: File
+        outputSource: index_bam/indexed_bam
+steps:
+    trim_and_align:
+        scatter: [sequence]
+        scatterMethod: dotproduct
+        run: sequence_to_bisulfite_alignment_adapter.cwl
+        in:
+            sequence: sequence
+            trimming_options: trimming_options
+            reference_index: reference_index
+        out:
+            [aligned_bam]
+    merge:
+        run: ../tools/merge_bams_samtools.cwl
+        in:
+            bams: trim_and_align/aligned_bam
+            name: sample_name
+        out:
+            [merged_bam]
+    name_sort:
+        run: ../tools/name_sort.cwl
+        in:
+            bam: merge/merged_bam
+        out:
+            [name_sorted_bam]
+    biscuit_markdup:
+        run: ../tools/biscuit_markdup.cwl
+        in:
+           bam: name_sort/name_sorted_bam
+        out:
+            [markdup_bam]
+    index_bam:
+        run: ../tools/index_bam.cwl
+        in:
+            bam: biscuit_markdup/markdup_bam
+        out:
+            [indexed_bam]

definitions/subworkflows/sequence_to_bisulfite_alignment_adapter.cwl

@@ -0,0 +1,48 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "adapter for sequence_to_biscuit_alignments"
+doc: "Some workflow engines won't stage files in our nested structure, so parse it out here"
+requirements:
+    - class: InlineJavascriptRequirement
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/sequence_data.yml
+          - $import: ../types/trimming_options.yml
+    - class: StepInputExpressionRequirement
+    - class: SubworkflowFeatureRequirement
+inputs:
+    sequence:
+        type: ../types/sequence_data.yml#sequence_data
+        doc: "the unaligned sequence data with readgroup information"
+    trimming_options:
+        type:
+            - ../types/trimming_options.yml#trimming_options
+            - "null"
+    reference_index:
+        type: string
+outputs:
+    aligned_bam:
+        type: File
+        outputSource: biscuit_align/aligned_bam
+steps:
+     biscuit_align:
+        run: ../tools/biscuit_align.cwl
+        in:
+            bam:
+                source: sequence
+                valueFrom: "$(self.sequence.hasOwnProperty('bam')? self.sequence.bam : null)"
+            fastq1:
+                source: sequence
+                valueFrom: "$(self.sequence.hasOwnProperty('fastq1')? self.sequence.fastq1 : null)"
+            fastq2:
+                source: sequence
+                valueFrom: "$(self.sequence.hasOwnProperty('fastq2')? self.sequence.fastq2 : null)"
+            read_group:
+                source: sequence
+                valueFrom: $(self.readgroup)
+            trimming_options: trimming_options
+            reference_index: reference_index
+        out:
+            [aligned_bam]