germline joint detect variants workflow

definitions/pipelines/germline_wgs.cwl

@@ -152,6 +152,11 @@ inputs:
     disclaimer_text:
         type: string?
         default: 'Workflow source can be found at https://github.com/genome/analysis-workflows'
+    annotsv_annotations:
+        type:
+            - string
+            - Directory
+        doc: "directory/path of the annotsv annotations directory"
 outputs:
     cram:
         type: File
@@ -468,6 +473,7 @@ steps:
             sv_split_count: sv_filter_split_count
             genome_build: vep_ensembl_assembly
             blocklist_bedpe: blocklist_bedpe
+            annotsv_annotations: annotsv_annotations
         out: 
            [cn_diagram, cn_scatter_plot, tumor_antitarget_coverage, tumor_target_coverage, tumor_bin_level_ratios, tumor_segmented_ratios, cnvkit_vcf, cnvnator_cn_file, cnvnator_root, cnvnator_vcf, manta_diploid_variants, manta_somatic_variants, manta_all_candidates, manta_small_candidates, manta_tumor_only_variants, smoove_output_variants, cnvkit_filtered_vcf, cnvnator_filtered_vcf, manta_filtered_vcf, smoove_filtered_vcf, survivor_merged_vcf, survivor_merged_annotated_tsv, bcftools_merged_vcf, bcftools_merged_annotated_tsv, bcftools_merged_filtered_annotated_tsv]
     add_disclaimer_survivor_sv_vcf:

definitions/subworkflows/gatk_soft_filter.cwl

@@ -0,0 +1,86 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "apply soft filtering to a gatk called vcf using hard filter parameters"
+requirements:
+    - class: SubworkflowFeatureRequirement
+    - class: StepInputExpressionRequirement
+    - class: MultipleInputFeatureRequirement
+inputs:
+    reference:
+        type:
+            - string
+            - File
+        secondaryFiles: [.fai, ^.dict]
+    vcf:
+        type: File
+        secondaryFiles: [.tbi]
+    output_basename:
+        type: string?
+        default: "soft_filtered"
+outputs:
+    filtered_vcf:
+        type: File
+        secondaryFiles: [.tbi]
+        outputSource: index_merged/indexed_vcf
+steps:
+    split_snps:
+        run: ../tools/select_variants.cwl
+        in:
+            reference: reference
+            vcf: vcf
+            output_vcf_basename:
+                default: "SNPS"
+            select_type:
+                default: "SNP"
+        out:
+            [filtered_vcf]
+    split_indels:
+        run: ../tools/select_variants.cwl
+        in:
+            reference: reference
+            vcf: vcf
+            output_vcf_basename:
+                default: "INDELS"
+            select_type:
+                default: "INDEL"
+        out:
+            [filtered_vcf]
+    filter_snps:
+        run: ../tools/variant_filtration.cwl
+        in:
+            reference: reference
+            vcf: split_snps/filtered_vcf
+            filters:
+                default: ["QD<2.0;QD2", "QUAL<30.0;QUAL30", "SOR>3.0;SOR3", "FS>60.0;FS60", "MQ<40.0;MQ40", "MQRankSum<-12.5;MQRankSum-12.5", "ReadPosRankSum<-8.0;ReadPosRankSum-8"]
+            output_vcf_basename:
+                default: "SNPS.filtered"
+        out:
+            [filtered_vcf]
+    filter_indels:
+        run: ../tools/variant_filtration.cwl
+        in:
+            reference: reference
+            vcf: split_indels/filtered_vcf
+            filters:
+                default: ["QD<2.0;QD2", "QUAL<30.0;QUAL30", "FS>200.0;FS200", "ReadPosRankSum<-20.0;ReadPosRankSum-20"]
+            output_vcf_basename:
+                default: "INDELS.filtered"
+        out:
+            [filtered_vcf]
+    merge:
+        run: ../tools/merge_vcf.cwl
+        in:
+            merged_vcf_basename: output_basename
+            vcfs:
+                source: [filter_snps/filtered_vcf, filter_indels/filtered_vcf]
+                linkMerge: merge_flattened
+        out:
+            [merged_vcf]
+    index_merged:
+        run: ../tools/index_vcf.cwl
+        in:
+            vcf: merge/merged_vcf
+        out:
+            [indexed_vcf]

definitions/subworkflows/joint_cnvkit.cwl

@@ -0,0 +1,92 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "jointly run cnvkit for sv calls"
+requirements:
+    - class: SubworkflowFeatureRequirement
+    - class: StepInputExpressionRequirement
+    - class: InlineJavascriptRequirement
+    - class: ScatterFeatureRequirement
+inputs:
+    sample_names:
+        type: string[]
+    bams:
+        type: File[]
+        secondaryFiles: [^.bai]
+    reference_fasta:
+        type:
+            - string
+            - File
+        secondaryFiles: [.fai]
+    reference_cnn:
+        type: File?
+        doc: "can be a flat reference or reference based on a panel of normals"
+    method:
+        type:
+          - "null"
+          - type: enum
+            symbols: ["hybrid", "amplicon", "wgs"]
+    segment_filter:
+        type:
+          - "null"
+          - type: enum
+            symbols: ["ampdel", "ci", "cn", "sem"]
+outputs:
+    vcfs:
+        type: File[]
+        outputSource: index_cnvkit/indexed_vcf
+        secondaryFiles: [.tbi]
+    cnr:
+        type: File[]
+        outputSource: cnvkit/tumor_bin_level_ratios
+    cns:
+        type: File[]
+        outputSource: cnvkit/tumor_segmented_ratios
+steps:
+    cnvkit:
+        scatter: [tumor_bam, cnvkit_vcf_name]
+        scatterMethod: dotproduct
+        run: cnvkit_single_sample.cwl
+        in:
+            method: method
+            reference_cnn: reference_cnn
+            tumor_bam: bams
+            cnvkit_vcf_name:
+                source: [sample_names]
+                valueFrom: "$(self).cnvkit.vcf"
+            segment_filter: segment_filter
+            fasta_reference: reference_fasta
+        out:
+            [tumor_bin_level_ratios, tumor_segmented_ratios, cnvkit_vcf]
+    bgzip_and_index:
+        scatter: [vcf]
+        run: bgzip_and_index.cwl
+        in:
+            vcf: cnvkit/cnvkit_vcf
+        out:
+            [indexed_vcf]
+    sample_rename:
+        scatter: [input_vcf, new_sample_name]
+        scatterMethod: dotproduct
+        run: ../tools/replace_vcf_sample_name.cwl
+        in:
+            input_vcf: bgzip_and_index/indexed_vcf
+            new_sample_name: sample_names
+            sample_to_replace:
+                valueFrom: 'adjusted.tumor'
+            output_name:
+                valueFrom: '${
+                    var sample = inputs.new_sample_name;
+                    var name = sample + ".cnvkit.vcf.gz";
+                    return name;
+                }'
+        out:
+            [renamed_vcf]
+    index_cnvkit:
+        scatter: [vcf]
+        run: ../tools/index_vcf.cwl
+        in:
+            vcf: sample_rename/renamed_vcf
+        out:
+            [indexed_vcf]

definitions/subworkflows/joint_cnvnator.cwl

@@ -0,0 +1,79 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: Workflow
+label: "run cnvnator for multiple samples"
+requirements:
+    - class: SubworkflowFeatureRequirement
+    - class: ScatterFeatureRequirement
+    - class: StepInputExpressionRequirement
+inputs:
+    reference:
+        type:
+            - string
+            - File
+        secondaryFiles: [.fai, ^.dict]
+    sample_names:
+        type: string[]
+    bams:
+        type: File[]
+        secondaryFiles: [^.bai]
+    bin_size:
+        type: int?
+outputs:
+    vcfs:
+        type: File[]
+        outputSource: index_cnvnator/indexed_vcf
+        secondaryFiles: [.tbi]
+    root_files:
+        type: File[]
+        outputSource: cnvnator/root_file
+    cn_files:
+        type: File[]
+        outputSource: cnvnator/cn_file
+steps:
+    cnvnator:
+        scatter: [bam, sample_name]
+        scatterMethod: dotproduct
+        run: ../tools/cnvnator.cwl
+        in:
+            bam: bams
+            reference: reference
+            sample_name: sample_names
+            bin_size: bin_size
+        out:
+            [vcf, root_file, cn_file]
+    bgzip_index:
+        scatter: [vcf]
+        run: bgzip_and_index.cwl
+        in:
+            vcf: cnvnator/vcf
+        out:
+            [indexed_vcf]
+    sample_rename:
+        scatter: [input_vcf, new_sample_name]
+        scatterMethod: dotproduct
+        run: ../tools/replace_vcf_sample_name.cwl
+        in:
+            input_vcf: bgzip_index/indexed_vcf
+            new_sample_name: sample_names
+            sample_to_replace:
+                valueFrom: '${
+                    var old_name = inputs.new_sample_name.split(".")[0];
+                    return old_name;
+                }'
+            output_name:
+                valueFrom: '${
+                    var sample = inputs.new_sample_name;
+                    var name = sample + ".cnvnator.vcf.gz";
+                    return name;
+                }'
+        out:
+            [renamed_vcf]
+    index_cnvnator:
+        scatter: [vcf]
+        run: ../tools/index_vcf.cwl
+        in:
+            vcf: sample_rename/renamed_vcf
+        out:
+            [indexed_vcf]