/
somatic_exome.cwl
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somatic_exome.cwl
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#!/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: MT sequencing data and readgroup information"
doc: |
tumor_sequence represents the sequencing data for the MT sample as either FASTQs or BAMs with
accompanying readgroup information. 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 example the VCF files.
normal_sequence:
type: ../types/sequence_data.yml#sequence_data[]
label: "normal_sequence: WT sequencing data and readgroup information"
doc: |
normal_sequence represents the sequencing data for the WT sample as either FASTQs or BAMs with
accompanying readgroup information. 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 example 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 (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
validated_variants:
type: File?
secondaryFiles: [.tbi]
doc: "An optional VCF with variants that will be flagged as 'VALIDATED' if found in this pipeline's main 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
validated_variants: validated_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]