#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Whole genome alignment and somatic variant detection"
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
inputs:
reference: string
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'
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'
trimming:
type:
- ../types/trimming_options.yml#trimming_options
- "null"
bqsr_known_sites:
type: File[]
secondaryFiles: [.tbi]
doc: "One or more databases of known polymorphic sites used to exclude regions around known polymorphisms from analysis."
bqsr_intervals:
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[]
qc_intervals:
type: File
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]
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
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?
annotate_coding_only:
type: boolean?
vep_pick:
type:
- "null"
- type: enum
symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"]
cle_vcf_filter:
type: boolean
default: false
variants_to_table_fields:
type: string[]
default: [CHROM,POS,ID,REF,ALT,set,AC,AF]
variants_to_table_genotype_fields:
type: string[]
default: [GT,AD]
vep_to_table_fields:
type: string[]
default: [HGVSc,HGVSp]
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]
manta_non_wgs:
type: boolean?
default: false
manta_output_contigs:
type: boolean?
somalier_vcf:
type: File
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"
cnvkit_target_average_size:
type: int?
doc: "approximate size of split target bins for CNVkit; if not set a suitable window size will be set by CNVkit automatically"
outputs:
##tumor alignment and QC
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_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
tumor_insert_size_histogram:
type: File
outputSource: tumor_alignment_and_qc/insert_size_histogram
tumor_gc_bias_metrics:
type: File
outputSource: tumor_alignment_and_qc/gc_bias_metrics
tumor_gc_bias_metrics_chart:
type: File
outputSource: tumor_alignment_and_qc/gc_bias_metrics_chart
tumor_gc_bias_metrics_summary:
type: File
outputSource: tumor_alignment_and_qc/gc_bias_metrics_summary
tumor_wgs_metrics:
type: File
outputSource: tumor_alignment_and_qc/wgs_metrics
##normal alignment and qc
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_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
normal_insert_size_histogram:
type: File
outputSource: normal_alignment_and_qc/insert_size_histogram
normal_gc_bias_metrics:
type: File
outputSource: normal_alignment_and_qc/gc_bias_metrics
normal_gc_bias_metrics_chart:
type: File
outputSource: normal_alignment_and_qc/gc_bias_metrics_chart
normal_gc_bias_metrics_summary:
type: File
outputSource: normal_alignment_and_qc/gc_bias_metrics_summary
normal_wgs_metrics:
type: File
outputSource: normal_alignment_and_qc/wgs_metrics
##variant calling
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]
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
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]
##sample concordance check
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_wgs.cwl
in:
reference: reference
sequence: tumor_sequence
trimming: trimming
omni_vcf: omni_vcf
intervals: qc_intervals
picard_metric_accumulation_level: picard_metric_accumulation_level
bqsr_known_sites: bqsr_known_sites
bqsr_intervals: bqsr_intervals
minimum_mapping_quality: qc_minimum_mapping_quality
minimum_base_quality: qc_minimum_base_quality
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
sample_name: tumor_name
out:
[alignment_summary_metrics, bam, flagstats, gc_bias_metrics_chart, gc_bias_metrics_summary, gc_bias_metrics, insert_size_histogram, insert_size_metrics, mark_duplicates_metrics, per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics, verify_bam_id_depth, verify_bam_id_metrics, wgs_metrics]
normal_alignment_and_qc:
run: alignment_wgs.cwl
in:
reference: reference
sequence: normal_sequence
trimming: trimming
omni_vcf: omni_vcf
intervals: qc_intervals
picard_metric_accumulation_level: picard_metric_accumulation_level
bqsr_known_sites: bqsr_known_sites
bqsr_intervals: bqsr_intervals
minimum_mapping_quality: qc_minimum_mapping_quality
minimum_base_quality: qc_minimum_base_quality
per_base_intervals: per_base_intervals
per_target_intervals: per_target_intervals
summary_intervals: summary_intervals
sample_name: normal_name
out:
[alignment_summary_metrics, bam, flagstats, gc_bias_metrics_chart, gc_bias_metrics_summary, gc_bias_metrics, insert_size_histogram, insert_size_metrics, mark_duplicates_metrics, per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics, verify_bam_id_depth, verify_bam_id_metrics, wgs_metrics]
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]
detect_variants:
run: detect_variants_wgs.cwl
in:
reference: reference
tumor_bam: tumor_alignment_and_qc/bam
normal_bam: normal_alignment_and_qc/bam
roi_intervals: target_intervals
strelka_exome_mode:
default: false
strelka_cpu_reserved: strelka_cpu_reserved
scatter_count: scatter_count
mutect_artifact_detection_mode: mutect_artifact_detection_mode
mutect_max_alt_allele_in_normal_fraction: mutect_max_alt_allele_in_normal_fraction
mutect_max_alt_alleles_in_normal_count: mutect_max_alt_alleles_in_normal_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, 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
method:
default: 'wgs'
reference:
source: [normal_alignment_and_qc/bam, reference]
valueFrom: |
${
var normal = self[0];
var fasta = self[1];
return {'normal_bam': normal, 'fasta_file': fasta};
}
target_average_size: cnvkit_target_average_size
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
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]