somatic_exome.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
requirements:
    - class: SchemaDefRequirement
      types:
          - $import: ../types/labelled_file.yml
          - $import: ../types/sequence_data.yml
          - $import: ../types/trimming_options.yml
          - $import: ../types/vep_custom_annotation.yml
    - class: SubworkflowFeatureRequirement
    - class: StepInputExpressionRequirement
label: "somatic_exome: exome alignment and somatic variant detection"
doc: |
  somatic_exome is designed to perform processing of mutant/wildtype H.sapiens
  exome sequencing data. It features BQSR corrected alignments, 4 caller variant
  detection, and vep style annotations. Structural variants are detected via
  manta and cnvkit. In addition QC metrics are run, including
  somalier concordance metrics.

  example input file = analysis_workflows/example_data/somatic_exome.yaml

inputs:
    reference:
        type:
            - string
            - File
        secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
        label: "reference: Reference fasta file for a desired assembly"
        doc: |
          reference contains the nucleotide sequence for a given assembly (hg37, hg38, etc.)
          in fasta format for the entire genome. This is what reads will be aligned to.
          Appropriate files can be found on ensembl at https://ensembl.org/info/data/ftp/index.html
          When providing the reference secondary files corresponding to reference indices must be
          located in the same directory as the reference itself. These files can be created with
          samtools index, bwa index, and picard CreateSequenceDictionary.
    tumor_sequence:
        type: ../types/sequence_data.yml#sequence_data[]
        label: "tumor_sequence: yml file specifying the location of MT sequencing data"
        doc: |
          tumor_sequence is a yml file for which to pass information regarding
          sequencing data for single sample (i.e. fastq files). If more than one fastq file exist
          for a sample, as in the case for multiple instrument data, the sequence tag is simply
          repeated with the additional data (see example input file). Note that in the @RG field
          ID and SM are required.
    tumor_name:
        type: string?
        default: 'tumor'
        label: "tumor_name: String specifying the name of the MT sample"
        doc: |
          tumor_name provides a string for what the MT sample will be referred to in the various
          outputs, for exmaple the VCF files.
    normal_sequence:
        type: ../types/sequence_data.yml#sequence_data[]
        label: "normal_sequence: yml file specifying the location of WT sequencing data"
        doc: |
          normal_sequence is a yml file for which to pass information regarding
          sequencing data for single sample (i.e. fastq files). If more than one fastq file exist
          for a sample, as in the case for multiple instrument data, the sequence tag is simply
          repeated with the additional data (see example input file). Note that in the @RG field
          ID and SM are required.
    normal_name:
        type: string?
        default: 'normal'
        label: "normal_name: String specifying the name of the WT sample"
        doc: |
          normal_name provides a string for what the WT sample will be referred to in the various
          outputs, for exmaple the VCF files.
    trimming:
        type:
            - ../types/trimming_options.yml#trimming_options
            - "null"
    mills:
        type: File
        secondaryFiles: [.tbi]
        label: "mills: File specifying common polymorphic indels from mills et al."
        doc: |
          mills provides known polymorphic indels recommended by GATK for a variety of
          tools including the BaseRecalibrator. This file is part of the GATK resource
          bundle available at http://www.broadinstitute.org/gatk/guide/article?id=1213
          Essentially it is a list of known indels originally discovered by mill et al.
          https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1557762/
          File should be in vcf format, and tabix indexed.
    known_indels:
        type: File
        secondaryFiles: [.tbi]
        label: "known_indels: File specifying common polymorphic indels from 1000G"
        doc: |
          known_indels provides known indels reecommended by GATK for a variety of tools
          including the BaseRecalibrator. This file is part of the GATK resource bundle
          available at http://www.broadinstitute.org/gatk/guide/article?id=1213
          Essintially it is a list of known indels from 1000 Genomes Phase I indel calls.
          File should be in vcf format, and tabix indexed.
    dbsnp_vcf:
        type: File
        secondaryFiles: [.tbi]
        label: "dbsnp_vcf: File specifying common polymorphic indels from dbSNP"
        doc: |
          dbsnp_vcf provides known indels reecommended by GATK for a variety of tools
          including the BaseRecalibrator. This file is part of the GATK resource bundle
          available at http://www.broadinstitute.org/gatk/guide/article?id=1213
          Essintially it is a list of known indels from dbSNP. File should be in vcf format,
          and tabix indexed.
    bqsr_intervals:
        type: string[]
        label: "bqsr_intervals: Array of strings specifying regions for base quality score recalibration"
        doc: |
          bqsr_intervals provides an array of genomic intervals for which to apply
          GATK base quality score recalibrations. Typically intervals are given
          for the entire chromosome (i.e. chr1, chr2, etc.), these names should match
          the format in the reference file.
    bait_intervals:
        type: File
        label: "bait_intervals: interval_list file of baits used in the sequencing experiment"
        doc: |
          bait_intervals is an interval_list corresponding to the baits used in sequencing reagent.
          These are essentially coordinates for regions you were able to design probes for in the reagent.
          Typically the reagent provider has this information available in bed format and it can be
          converted to an interval_list with Picard BedToIntervalList. Astrazeneca also maintains a repo
          of baits for common sequencing reagents available at https://github.com/AstraZeneca-NGS/reference_data
    target_intervals:
        type: File
        label: "target_intervals: interval_list file of targets used in the sequencing experiment"
        doc: |
          target_intervals is an interval_list corresponding to the targets for the capture reagent.
          Bed files with this information can be converted to interval_lists with Picard BedToIntervalList.
          In general for a WES exome reagent bait_intervals and target_intervals are the same.
    target_interval_padding:
        type: int
        label: "target_interval_padding: number of bp flanking each target region in which to allow variant calls"
        doc: |
            The effective coverage of capture products generally extends out beyond the actual regions
            targeted. This parameter allows variants to be called in these wingspan regions, extending
            this many base pairs from each side of the target regions.
        default: 100
    per_base_intervals:
        type: ../types/labelled_file.yml#labelled_file[]
        label: "per_base_intervals: additional intervals over which to summarize coverage/QC at a per-base resolution"
        doc: "per_base_intervals is a list of regions (in interval_list format) over which to summarize coverage/QC at a per-base resolution."
    per_target_intervals:
        type: ../types/labelled_file.yml#labelled_file[]
        label: "per_target_intervals: additional intervals over which to summarize coverage/QC at a per-target resolution"
        doc: "per_target_intervals list of regions (in interval_list format) over which to summarize coverage/QC at a per-target resolution."
    summary_intervals:
        type: ../types/labelled_file.yml#labelled_file[]
    omni_vcf:
        type: File
        secondaryFiles: [.tbi]
    picard_metric_accumulation_level:
        type: string
    qc_minimum_mapping_quality:
        type: int?
        default: 0
    qc_minimum_base_quality:
        type: int?
        default: 0
    cosmic_vcf:
        type: File?
        secondaryFiles: [.tbi]
    panel_of_normals_vcf:
        type: File?
        secondaryFiles: [.tbi]
    strelka_cpu_reserved:
        type: int?
        default: 8
    mutect_scatter_count:
        type: int
    mutect_artifact_detection_mode:
        type: boolean
        default: false
    mutect_max_alt_allele_in_normal_fraction:
        type: float?
    mutect_max_alt_alleles_in_normal_count:
        type: int?
    varscan_strand_filter:
        type: int?
        default: 0
    varscan_min_coverage:
        type: int?
        default: 8
    varscan_min_var_freq:
        type: float?
        default: 0.05
    varscan_p_value:
        type: float?
        default: 0.99
    varscan_max_normal_freq:
        type: float?
    pindel_insert_size:
        type: int
        default: 400
    docm_vcf:
        type: File
        secondaryFiles: [.tbi]
        doc: "The set of alleles that gatk haplotype caller will use to force-call regardless of evidence"
    filter_docm_variants:
        type: boolean?
        default: true
    vep_cache_dir:
        type:
            - string
            - Directory
        doc: "path to the vep cache directory, available at: https://useast.ensembl.org/info/docs/tools/vep/script/vep_cache.html#pre"
    vep_ensembl_assembly:
        type: string
        doc: "genome assembly to use in vep. Examples: GRCh38 or GRCm38"
    vep_ensembl_version:
        type: string
        doc: "ensembl version - Must be present in the cache directory. Example: 95"
    vep_ensembl_species:
        type: string
        doc: "ensembl species - Must be present in the cache directory. Examples: homo_sapiens or mus_musculus"
    synonyms_file:
        type: File?
        doc: "synonyms_file allows the use of different chromosome identifiers in vep inputs or annotation files (cache, database, GFF, custom file, fasta). File should be tab-delimited with the primary identifier in column 1 and the synonym in column 2."
    annotate_coding_only:
        type: boolean?
        doc: "if set to true, vep only returns consequences that fall in the coding regions of transcripts"
    vep_pick:
        type:
            - "null"
            - type: enum
              symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"]
        doc: "configures how vep will annotate genomic features that each variant overlaps; for a detailed description of each option see https://useast.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick_allele_gene_eg"
    cle_vcf_filter:
        type: boolean
        default: false
    variants_to_table_fields:
        type: string[]
        default: [CHROM,POS,ID,REF,ALT,set,AC,AF]
        doc: "The names of one or more standard VCF fields or INFO fields to include in the output table"
    variants_to_table_genotype_fields:
        type: string[]
        default: [GT,AD]
        doc: "The name of a genotype field to include in the output table"
    vep_to_table_fields:
        type: string[]
        default: [HGVSc,HGVSp]
        doc: "VEP fields in final output"
    vep_custom_annotations:
        type: ../types/vep_custom_annotation.yml#vep_custom_annotation[]
        doc: "custom type, check types directory for input format"
    manta_call_regions:
        type: File?
        secondaryFiles: [.tbi]
        doc: "bgzip-compressed, tabix-indexed BED file specifiying regions to which manta structural variant analysis is limited"
    manta_non_wgs:
        type: boolean?
        default: true
        doc: "toggles on or off manta settings for WES vs. WGS mode for structural variant detection"
    manta_output_contigs:
        type: boolean?
        doc: "if set to true configures manta to output assembled contig sequences in the final VCF files"
    somalier_vcf:
        type: File
        doc: "a vcf file of known polymorphic sites for somalier to compare normal and tumor samples for identity; sites files can be found at: https://github.com/brentp/somalier/releases"
    tumor_sample_name:
        type: string
    normal_sample_name:
        type: string
    known_variants:
        type: File?
        secondaryFiles: [.tbi]
        doc: "Previously discovered variants to be flagged in this pipelines's output vcf"
outputs:
    tumor_cram:
        type: File
        outputSource: tumor_index_cram/indexed_cram
    tumor_mark_duplicates_metrics:
        type: File
        outputSource: tumor_alignment_and_qc/mark_duplicates_metrics
    tumor_insert_size_metrics:
        type: File
        outputSource: tumor_alignment_and_qc/insert_size_metrics
    tumor_alignment_summary_metrics:
        type: File
        outputSource: tumor_alignment_and_qc/alignment_summary_metrics
    tumor_hs_metrics:
        type: File
        outputSource: tumor_alignment_and_qc/hs_metrics
    tumor_per_target_coverage_metrics:
        type: File[]
        outputSource: tumor_alignment_and_qc/per_target_coverage_metrics
    tumor_per_target_hs_metrics:
        type: File[]
        outputSource: tumor_alignment_and_qc/per_target_hs_metrics
    tumor_per_base_coverage_metrics:
        type: File[]
        outputSource: tumor_alignment_and_qc/per_base_coverage_metrics
    tumor_per_base_hs_metrics:
        type: File[]
        outputSource: tumor_alignment_and_qc/per_base_hs_metrics
    tumor_summary_hs_metrics:
        type: File[]
        outputSource: tumor_alignment_and_qc/summary_hs_metrics
    tumor_flagstats:
        type: File
        outputSource: tumor_alignment_and_qc/flagstats
    tumor_verify_bam_id_metrics:
        type: File
        outputSource: tumor_alignment_and_qc/verify_bam_id_metrics
    tumor_verify_bam_id_depth:
        type: File
        outputSource: tumor_alignment_and_qc/verify_bam_id_depth
    normal_cram:
        type: File
        outputSource: normal_index_cram/indexed_cram
    normal_mark_duplicates_metrics:
        type: File
        outputSource: normal_alignment_and_qc/mark_duplicates_metrics
    normal_insert_size_metrics:
        type: File
        outputSource: normal_alignment_and_qc/insert_size_metrics
    normal_alignment_summary_metrics:
        type: File
        outputSource: normal_alignment_and_qc/alignment_summary_metrics
    normal_hs_metrics:
        type: File
        outputSource: normal_alignment_and_qc/hs_metrics
    normal_per_target_coverage_metrics:
        type: File[]
        outputSource: normal_alignment_and_qc/per_target_coverage_metrics
    normal_per_target_hs_metrics:
        type: File[]
        outputSource: normal_alignment_and_qc/per_target_hs_metrics
    normal_per_base_coverage_metrics:
        type: File[]
        outputSource: normal_alignment_and_qc/per_base_coverage_metrics
    normal_per_base_hs_metrics:
        type: File[]
        outputSource: normal_alignment_and_qc/per_base_hs_metrics
    normal_summary_hs_metrics:
        type: File[]
        outputSource: normal_alignment_and_qc/summary_hs_metrics
    normal_flagstats:
        type: File
        outputSource: normal_alignment_and_qc/flagstats
    normal_verify_bam_id_metrics:
        type: File
        outputSource: normal_alignment_and_qc/verify_bam_id_metrics
    normal_verify_bam_id_depth:
        type: File
        outputSource: normal_alignment_and_qc/verify_bam_id_depth
    mutect_unfiltered_vcf:
        type: File
        outputSource: detect_variants/mutect_unfiltered_vcf
        secondaryFiles: [.tbi]
    mutect_filtered_vcf:
        type: File
        outputSource: detect_variants/mutect_filtered_vcf
        secondaryFiles: [.tbi]
    strelka_unfiltered_vcf:
        type: File
        outputSource: detect_variants/strelka_unfiltered_vcf
        secondaryFiles: [.tbi]
    strelka_filtered_vcf:
        type: File
        outputSource: detect_variants/strelka_filtered_vcf
        secondaryFiles: [.tbi]
    varscan_unfiltered_vcf:
        type: File
        outputSource: detect_variants/varscan_unfiltered_vcf
        secondaryFiles: [.tbi]
    varscan_filtered_vcf:
        type: File
        outputSource: detect_variants/varscan_filtered_vcf
        secondaryFiles: [.tbi]
    pindel_unfiltered_vcf:
        type: File
        outputSource: detect_variants/pindel_unfiltered_vcf
        secondaryFiles: [.tbi]
    pindel_filtered_vcf:
        type: File
        outputSource: detect_variants/pindel_filtered_vcf
        secondaryFiles: [.tbi]
    docm_filtered_vcf:
        type: File
        outputSource: detect_variants/docm_filtered_vcf
        secondaryFiles: [.tbi]
    final_vcf:
        type: File
        outputSource: detect_variants/final_vcf
        secondaryFiles: [.tbi]
    final_filtered_vcf:
        type: File
        outputSource: detect_variants/final_filtered_vcf
        secondaryFiles: [.tbi]
    final_tsv:
        type: File
        outputSource: detect_variants/final_tsv
    vep_summary:
        type: File
        outputSource: detect_variants/vep_summary
    tumor_snv_bam_readcount_tsv:
        type: File
        outputSource: detect_variants/tumor_snv_bam_readcount_tsv
    tumor_indel_bam_readcount_tsv:
        type: File
        outputSource: detect_variants/tumor_indel_bam_readcount_tsv
    normal_snv_bam_readcount_tsv:
        type: File
        outputSource: detect_variants/normal_snv_bam_readcount_tsv
    normal_indel_bam_readcount_tsv:
        type: File
        outputSource: detect_variants/normal_indel_bam_readcount_tsv
    intervals_antitarget:
        type: File?
        outputSource: cnvkit/intervals_antitarget
    intervals_target:
        type: File?
        outputSource: cnvkit/intervals_target
    normal_antitarget_coverage:
        type: File
        outputSource: cnvkit/normal_antitarget_coverage
    normal_target_coverage:
        type: File
        outputSource: cnvkit/normal_target_coverage
    reference_coverage:
        type: File?
        outputSource: cnvkit/reference_coverage
    cn_diagram:
        type: File?
        outputSource: cnvkit/cn_diagram
    cn_scatter_plot:
        type: File?
        outputSource: cnvkit/cn_scatter_plot
    tumor_antitarget_coverage:
        type: File
        outputSource: cnvkit/tumor_antitarget_coverage
    tumor_target_coverage:
        type: File
        outputSource: cnvkit/tumor_target_coverage
    tumor_bin_level_ratios:
        type: File
        outputSource: cnvkit/tumor_bin_level_ratios
    tumor_segmented_ratios:
        type: File
        outputSource: cnvkit/tumor_segmented_ratios
    diploid_variants:
        type: File?
        outputSource: manta/diploid_variants
        secondaryFiles: [.tbi]
    somatic_variants:
        type: File?
        outputSource: manta/somatic_variants
        secondaryFiles: [.tbi]
    all_candidates:
        type: File
        outputSource: manta/all_candidates
        secondaryFiles: [.tbi]
    small_candidates:
        type: File
        outputSource: manta/small_candidates
        secondaryFiles: [.tbi]
    tumor_only_variants:
        type: File?
        outputSource: manta/tumor_only_variants
        secondaryFiles: [.tbi]
    somalier_concordance_metrics:
        type: File
        outputSource: concordance/somalier_pairs
    somalier_concordance_statistics:
        type: File
        outputSource: concordance/somalier_samples
steps:
    tumor_alignment_and_qc:
        run: alignment_exome.cwl
        in:
            reference: reference
            sequence: tumor_sequence
            trimming: trimming
            mills: mills
            known_indels: known_indels
            dbsnp_vcf: dbsnp_vcf
            bqsr_intervals: bqsr_intervals
            bait_intervals: bait_intervals
            target_intervals: target_intervals
            per_base_intervals: per_base_intervals
            per_target_intervals: per_target_intervals
            summary_intervals: summary_intervals
            omni_vcf: omni_vcf
            picard_metric_accumulation_level: picard_metric_accumulation_level
            qc_minimum_mapping_quality: qc_minimum_mapping_quality
            qc_minimum_base_quality: qc_minimum_base_quality
            final_name:
                source: tumor_name
                valueFrom: "$(self).bam"
        out:
            [bam, mark_duplicates_metrics, insert_size_metrics, alignment_summary_metrics, hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, per_base_coverage_metrics, per_base_hs_metrics, summary_hs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth]
    normal_alignment_and_qc:
        run: alignment_exome.cwl
        in:
            reference: reference
            sequence: normal_sequence
            trimming: trimming
            mills: mills
            known_indels: known_indels
            dbsnp_vcf: dbsnp_vcf
            bqsr_intervals: bqsr_intervals
            bait_intervals: bait_intervals
            target_intervals: target_intervals
            per_base_intervals: per_base_intervals
            per_target_intervals: per_target_intervals
            summary_intervals: summary_intervals
            omni_vcf: omni_vcf
            picard_metric_accumulation_level: picard_metric_accumulation_level
            qc_minimum_mapping_quality: qc_minimum_mapping_quality
            qc_minimum_base_quality: qc_minimum_base_quality
            final_name:
                source: normal_name
                valueFrom: "$(self).bam"
        out:
            [bam, mark_duplicates_metrics, insert_size_metrics, 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, verify_bam_id_metrics, verify_bam_id_depth]
    concordance:
        run: ../tools/concordance.cwl
        in:
            reference: reference
            bam_1: tumor_alignment_and_qc/bam
            bam_2: normal_alignment_and_qc/bam
            vcf: somalier_vcf
        out:
            [somalier_pairs, somalier_samples]
    pad_target_intervals:
        run: ../tools/interval_list_expand.cwl
        in: 
            interval_list: target_intervals
            roi_padding: target_interval_padding
        out:
            [expanded_interval_list]
    detect_variants:
        run: detect_variants.cwl
        in:
            reference: reference
            tumor_bam: tumor_alignment_and_qc/bam
            normal_bam: normal_alignment_and_qc/bam
            roi_intervals: pad_target_intervals/expanded_interval_list
            strelka_exome_mode:
                default: true
            strelka_cpu_reserved: strelka_cpu_reserved
            mutect_scatter_count: mutect_scatter_count
            varscan_strand_filter: varscan_strand_filter
            varscan_min_coverage: varscan_min_coverage
            varscan_min_var_freq: varscan_min_var_freq
            varscan_p_value: varscan_p_value
            varscan_max_normal_freq: varscan_max_normal_freq
            pindel_insert_size: pindel_insert_size
            docm_vcf: docm_vcf
            filter_docm_variants: filter_docm_variants
            vep_cache_dir: vep_cache_dir
            vep_ensembl_assembly: vep_ensembl_assembly
            vep_ensembl_version: vep_ensembl_version
            vep_ensembl_species: vep_ensembl_species
            synonyms_file: synonyms_file
            annotate_coding_only: annotate_coding_only
            vep_pick: vep_pick
            cle_vcf_filter: cle_vcf_filter
            variants_to_table_fields: variants_to_table_fields
            variants_to_table_genotype_fields: variants_to_table_genotype_fields
            vep_to_table_fields: vep_to_table_fields
            tumor_sample_name: tumor_sample_name
            normal_sample_name: normal_sample_name
            vep_custom_annotations: vep_custom_annotations
            known_variants: known_variants
        out:
            [mutect_unfiltered_vcf, mutect_filtered_vcf, strelka_unfiltered_vcf, strelka_filtered_vcf, varscan_unfiltered_vcf, varscan_filtered_vcf, pindel_unfiltered_vcf, pindel_filtered_vcf, docm_filtered_vcf, final_vcf, final_filtered_vcf, final_tsv, vep_summary, tumor_snv_bam_readcount_tsv, tumor_indel_bam_readcount_tsv, normal_snv_bam_readcount_tsv, normal_indel_bam_readcount_tsv]
    cnvkit:
        run: ../tools/cnvkit_batch.cwl
        in:
            tumor_bam: tumor_alignment_and_qc/bam
            reference:
                source: [normal_alignment_and_qc/bam, reference]
                valueFrom: |
                    ${
                      var normal = self[0];
                      var fasta = self[1];
                      return {'normal_bam': normal, 'fasta_file': fasta};
                    }
            bait_intervals: bait_intervals
        out:
            [intervals_antitarget, intervals_target, normal_antitarget_coverage, normal_target_coverage, reference_coverage, cn_diagram, cn_scatter_plot, tumor_antitarget_coverage, tumor_target_coverage, tumor_bin_level_ratios, tumor_segmented_ratios]
    manta:
        run: ../tools/manta_somatic.cwl
        in:
            normal_bam: normal_alignment_and_qc/bam
            tumor_bam: tumor_alignment_and_qc/bam
            reference: reference
            call_regions: manta_call_regions
            non_wgs: manta_non_wgs
            output_contigs: manta_output_contigs
        out:
            [diploid_variants, somatic_variants, all_candidates, small_candidates, tumor_only_variants]
    tumor_bam_to_cram:
        run: ../tools/bam_to_cram.cwl
        in:
            bam: tumor_alignment_and_qc/bam
            reference: reference
        out:
            [cram]
    tumor_index_cram:
         run: ../tools/index_cram.cwl
         in:
            cram: tumor_bam_to_cram/cram
         out:
            [indexed_cram]
    normal_bam_to_cram:
        run: ../tools/bam_to_cram.cwl
        in:
            bam: normal_alignment_and_qc/bam
            reference: reference
        out:
            [cram]
    normal_index_cram:
         run: ../tools/index_cram.cwl
         in:
            cram: normal_bam_to_cram/cram
         out:
            [indexed_cram]