Update interval input

definitions/pipelines/simple_exome_alignment.cwl

@@ -0,0 +1,134 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "simple xome alignment with qc"
+requirements:
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/labelled_file.yml
+    - class: SubworkflowFeatureRequirement
+inputs:
+    reference: string
+    bams:
+        type: File[]
+    readgroups:
+        type: string[]
+    bait_intervals:
+        type: File
+    final_name:
+        type: string?
+    target_intervals:
+        type: File
+    per_base_intervals:
+        type: ../types/labelled_file.yml#labelled_file[]
+    per_target_intervals:
+        type: ../types/labelled_file.yml#labelled_file[]
+    summary_intervals:
+        type: ../types/labelled_file.yml#labelled_file[]
+    picard_metric_accumulation_level:
+        type: string
+    qc_minimum_mapping_quality:
+        type: int?
+    qc_minimum_base_quality:
+        type: int?
+outputs:
+    cram:
+        type: File
+        outputSource: index_cram/indexed_cram
+    mark_duplicates_metrics:
+        type: File
+        outputSource: mark_duplicates_and_sort/metrics_file
+    insert_size_metrics:
+        type: File
+        outputSource: qc/insert_size_metrics
+    insert_size_histogram:
+        type: File
+        outputSource: qc/insert_size_histogram
+    alignment_summary_metrics:
+        type: File
+        outputSource: qc/alignment_summary_metrics
+    hs_metrics:
+        type: File
+        outputSource: qc/hs_metrics
+    per_target_coverage_metrics:
+        type: File[]
+        outputSource: qc/per_target_coverage_metrics
+    per_target_hs_metrics:
+        type: File[]
+        outputSource: qc/per_target_hs_metrics
+    per_base_coverage_metrics:
+        type: File[]
+        outputSource: qc/per_base_coverage_metrics
+    per_base_hs_metrics:
+        type: File[]
+        outputSource: qc/per_base_hs_metrics
+    summary_hs_metrics:
+        type: File[]
+        outputSource: qc/summary_hs_metrics
+    flagstats:
+        type: File
+        outputSource: qc/flagstats
+steps:
+    align:
+        scatter: [bam, readgroup]
+        scatterMethod: dotproduct
+        run: align.cwl
+        in:
+            bam: bams
+            readgroup: readgroups
+            reference: reference
+        out:
+            [tagged_bam]
+    merge:
+        run: ../tools/merge_bams_samtools.cwl
+        in:
+            bams: align/tagged_bam
+            name: final_name
+        out:
+            [merged_bam]
+    name_sort:
+        run: ../tools/name_sort.cwl
+        in:
+            bam: merge/merged_bam
+        out:
+            [name_sorted_bam]
+    mark_duplicates_and_sort:
+        run: ../tools/mark_duplicates_and_sort.cwl
+        in:
+            bam: name_sort/name_sorted_bam
+        out:
+            [sorted_bam, metrics_file]
+    index_bam:
+        run: ../tools/index_bam.cwl
+        in:
+            bam: mark_duplicates_and_sort/sorted_bam
+        out:
+            [indexed_bam]
+    qc:
+        run: ../subworkflows/qc_exome_no_vbi.cwl
+        in:
+            bam: index_bam/indexed_bam
+            reference: reference
+            bait_intervals: bait_intervals
+            target_intervals: target_intervals
+            per_base_intervals: per_base_intervals
+            per_target_intervals: per_target_intervals
+            summary_intervals: summary_intervals
+            picard_metric_accumulation_level: picard_metric_accumulation_level
+            minimum_mapping_quality: qc_minimum_mapping_quality
+            minimum_base_quality: qc_minimum_base_quality
+        out: [insert_size_metrics, insert_size_histogram, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats]
+    bam_to_cram:
+        run: ../tools/bam_to_cram.cwl
+        in:
+            bam: index_bam/indexed_bam
+            reference: reference
+        out:
+            [cram]
+    index_cram:
+         run: ../tools/index_cram.cwl
+         in:
+            cram: bam_to_cram/cram
+         out:
+            [indexed_cram]

definitions/pipelines/wgs_alignment.cwl

@@ -26,7 +26,7 @@ inputs:
     omni_vcf:
         type: File
         secondaryFiles: [.tbi]
-    intervals:
+    qc_intervals:
         type: File
     picard_metric_accumulation_level:
         type: string
@@ -115,7 +115,7 @@ steps:
             bam: alignment/final_bam
             reference: reference
             omni_vcf: omni_vcf
-            intervals: intervals
+            intervals: qc_intervals
             picard_metric_accumulation_level: picard_metric_accumulation_level
             minimum_mapping_quality: minimum_mapping_quality
             minimum_base_quality: minimum_base_quality

definitions/subworkflows/qc_exome_no_vbi.cwl

@@ -0,0 +1,117 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "Exome QC workflow without VerifyBamId"
+requirements:
+    - class: SchemaDefRequirement
+      types:
+          - $import: ../types/labelled_file.yml
+    - class: SubworkflowFeatureRequirement
+inputs:
+    bam:
+        type: File
+        secondaryFiles: [^.bai]
+    reference:
+        type: string
+    bait_intervals:
+        type: File
+    target_intervals:
+        type: File
+    picard_metric_accumulation_level:
+        type: string?
+        default: ALL_READS
+    minimum_mapping_quality:
+        type: int?
+    minimum_base_quality:
+        type: int?
+    per_base_intervals:
+        type: ../types/labelled_file.yml#labelled_file[]
+    per_target_intervals:
+        type: ../types/labelled_file.yml#labelled_file[]
+    summary_intervals:
+        type: ../types/labelled_file.yml#labelled_file[]
+outputs:
+    insert_size_metrics:
+        type: File
+        outputSource: collect_insert_size_metrics/insert_size_metrics
+    insert_size_histogram:
+        type: File
+        outputSource: collect_insert_size_metrics/insert_size_histogram
+    alignment_summary_metrics:
+        type: File
+        outputSource: collect_alignment_summary_metrics/alignment_summary_metrics
+    hs_metrics:
+        type: File
+        outputSource: collect_roi_hs_metrics/hs_metrics
+    per_target_coverage_metrics:
+        type: File[]
+        outputSource: collect_detailed_hs_metrics/per_target_coverage_metrics
+    per_target_hs_metrics:
+        type: File[]
+        outputSource: collect_detailed_hs_metrics/per_target_hs_metrics
+    per_base_coverage_metrics:
+        type: File[]
+        outputSource: collect_detailed_hs_metrics/per_base_coverage_metrics
+    per_base_hs_metrics:
+        type: File[]
+        outputSource: collect_detailed_hs_metrics/per_base_hs_metrics
+    summary_hs_metrics:
+        type: File[]
+        outputSource: collect_detailed_hs_metrics/summary_hs_metrics
+    flagstats:
+        type: File
+        outputSource: samtools_flagstat/flagstats
+steps:
+    collect_insert_size_metrics:
+        run: ../tools/collect_insert_size_metrics.cwl
+        in:
+            bam: bam
+            reference: reference
+            metric_accumulation_level: picard_metric_accumulation_level
+        out:
+            [insert_size_metrics, insert_size_histogram]
+    collect_alignment_summary_metrics:
+        run: ../tools/collect_alignment_summary_metrics.cwl
+        in:
+            bam: bam
+            reference: reference
+            metric_accumulation_level: picard_metric_accumulation_level
+        out:
+            [alignment_summary_metrics]
+    collect_roi_hs_metrics:
+        run: ../tools/collect_hs_metrics.cwl
+        in:
+            bam: bam
+            reference: reference
+            metric_accumulation_level:
+                valueFrom: "ALL_READS"
+            bait_intervals: bait_intervals
+            target_intervals: target_intervals
+            per_target_coverage:
+                default: false
+            per_base_coverage:
+                default: false
+            output_prefix:
+                valueFrom: "roi"
+            minimum_mapping_quality: minimum_mapping_quality
+            minimum_base_quality: minimum_base_quality
+        out:
+            [hs_metrics]
+    collect_detailed_hs_metrics:
+        run: hs_metrics.cwl
+        in:
+            bam: bam
+            minimum_mapping_quality: minimum_mapping_quality
+            minimum_base_quality: minimum_base_quality
+            per_base_intervals: per_base_intervals
+            per_target_intervals: per_target_intervals
+            reference: reference
+            summary_intervals: summary_intervals
+        out:
+            [per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics]
+    samtools_flagstat:
+        run: ../tools/samtools_flagstat.cwl
+        in:
+            bam: bam
+        out: [flagstats]