#!/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: MultipleInputFeatureRequirement - 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" bqsr_known_sites: type: File[] secondaryFiles: [.tbi] label: "bqsr_known_sites: One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis." doc: | Known polymorphic indels recommended by GATK for a variety of tools including the BaseRecalibrator. This is part of the GATK resource bundle available at http://www.broadinstitute.org/gatk/guide/article?id=1213 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 strelka_cpu_reserved: type: int? default: 8 scatter_count: type: int doc: "scatters each supported variant detector (varscan, pindel, mutect) into this many parallel jobs" 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 filter_somatic_llr_threshold: type: float default: 5 doc: "Sets the stringency (log-likelihood ratio) used to filter out non-somatic variants. Typical values are 10=high stringency, 5=normal, 3=low stringency. Low stringency may be desirable when read depths are low (as in WGS) or when tumor samples are impure." filter_somatic_llr_tumor_purity: type: float default: 1 doc: "Sets the purity of the tumor used in the somatic llr filter, used to remove non-somatic variants. Probably only needs to be adjusted for low-purity (< 50%). Range is 0 to 1" filter_somatic_llr_normal_contamination_rate: type: float default: 0 doc: "Sets the fraction of tumor present in the normal sample (range 0 to 1), used in the somatic llr filter. Useful for heavily contaminated adjacent normals. Range is 0 to 1" 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 bqsr_known_sites: bqsr_known_sites 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 bqsr_known_sites: bqsr_known_sites 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 scatter_count: 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 filter_somatic_llr_threshold: filter_somatic_llr_threshold filter_somatic_llr_tumor_purity: filter_somatic_llr_tumor_purity filter_somatic_llr_normal_contamination_rate: filter_somatic_llr_normal_contamination_rate 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]