/
tumor_only_wgs.cwl
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tumor_only_wgs.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "wgs alignment and tumor-only 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
inputs:
reference:
type:
- string
- File
secondaryFiles: [.fai, ^.dict, .amb, .ann, .bwt, .pac, .sa]
sequence:
type: ../types/sequence_data.yml#sequence_data[]
label: "sequence: sequencing data and readgroup information"
doc: |
sequence represents the sequencing data as either FASTQs or BAMs with accompanying
readgroup information. Note that in the @RG field ID and SM are required.
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."
omni_vcf:
type: File
secondaryFiles: [.tbi]
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.
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 reagent. In the case of WGS
this generally should contain intervals that span the entire genome.
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[]
picard_metric_accumulation_level:
type: string
roi_intervals:
type: File
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?
vep_pick:
type:
- "null"
- type: enum
symbols: ["pick", "flag_pick", "pick_allele", "per_gene", "pick_allele_gene", "flag_pick_allele", "flag_pick_allele_gene"]
sample_name:
type: string
docm_vcf:
type: File
doc: "Common mutations in cancer that will be genotyped and passed through into the merged VCF if they have even low-level evidence of a mutation (by default, marked with filter DOCM_ONLY)"
vep_custom_annotations:
type: ../types/vep_custom_annotation.yml#vep_custom_annotation[]
doc: "custom type, check types directory for input format"
readcount_minimum_mapping_quality:
type: int?
readcount_minimum_base_quality:
type: int?
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]
varscan_min_coverage:
type: int?
default: 8
varscan_min_var_freq:
type: float?
default: 0.05
varscan_min_reads:
type: int?
default: 2
maximum_population_allele_frequency:
type: float?
default: 0.001
qc_minimum_mapping_quality:
type: int?
default: 0
qc_minimum_base_quality:
type: int?
default: 0
outputs:
cram:
type: File
outputSource: index_cram/indexed_cram
mark_duplicates_metrics:
type: File
outputSource: alignment_and_qc/mark_duplicates_metrics
insert_size_metrics:
type: File
outputSource: alignment_and_qc/insert_size_metrics
insert_size_histogram:
type: File
outputSource: alignment_and_qc/insert_size_histogram
alignment_summary_metrics:
type: File
outputSource: alignment_and_qc/alignment_summary_metrics
gc_bias_metrics:
type: File
outputSource: alignment_and_qc/gc_bias_metrics
gc_bias_metrics_chart:
type: File
outputSource: alignment_and_qc/gc_bias_metrics_chart
gc_bias_metrics_summary:
type: File
outputSource: alignment_and_qc/gc_bias_metrics_summary
wgs_metrics:
type: File
outputSource: alignment_and_qc/wgs_metrics
flagstats:
type: File
outputSource: alignment_and_qc/flagstats
verify_bam_id_metrics:
type: File
outputSource: alignment_and_qc/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: alignment_and_qc/verify_bam_id_depth
varscan_vcf:
type: File
outputSource: detect_variants/varscan_vcf
secondaryFiles: [.tbi]
docm_gatk_vcf:
type: File
outputSource: detect_variants/docm_gatk_vcf
annotated_vcf:
type: File
outputSource: detect_variants/annotated_vcf
secondaryFiles: [.tbi]
final_vcf:
type: File
outputSource: detect_variants/final_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
per_base_coverage_metrics:
type: File[]
outputSource: alignment_and_qc/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: alignment_and_qc/per_base_hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: alignment_and_qc/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: alignment_and_qc/per_target_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: alignment_and_qc/summary_hs_metrics
steps:
alignment_and_qc:
run: alignment_wgs.cwl
in:
reference: reference
sequence: sequence
trimming: trimming
omni_vcf: omni_vcf
intervals: target_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: sample_name
out:
[bam, mark_duplicates_metrics, insert_size_metrics, insert_size_histogram, alignment_summary_metrics, gc_bias_metrics, gc_bias_metrics_chart, gc_bias_metrics_summary, wgs_metrics, flagstats, verify_bam_id_metrics, verify_bam_id_depth, per_base_coverage_metrics, per_base_hs_metrics, per_target_coverage_metrics, per_target_hs_metrics, summary_hs_metrics]
detect_variants:
run: tumor_only_detect_variants.cwl
in:
reference: reference
bam: alignment_and_qc/bam
roi_intervals: roi_intervals
varscan_min_coverage: varscan_min_coverage
varscan_min_var_freq: varscan_min_var_freq
varscan_min_reads: varscan_min_reads
maximum_population_allele_frequency: maximum_population_allele_frequency
vep_cache_dir: vep_cache_dir
synonyms_file: synonyms_file
vep_pick: vep_pick
vep_ensembl_assembly: vep_ensembl_assembly
vep_ensembl_version: vep_ensembl_version
vep_ensembl_species: vep_ensembl_species
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
sample_name: sample_name
docm_vcf: docm_vcf
vep_custom_annotations: vep_custom_annotations
readcount_minimum_mapping_quality: readcount_minimum_mapping_quality
readcount_minimum_base_quality: readcount_minimum_base_quality
out:
[varscan_vcf, docm_gatk_vcf, annotated_vcf, final_vcf, final_tsv, vep_summary, tumor_snv_bam_readcount_tsv, tumor_indel_bam_readcount_tsv]
bam_to_cram:
run: ../tools/bam_to_cram.cwl
in:
bam: alignment_and_qc/bam
reference: reference
out:
[cram]
index_cram:
run: ../tools/index_cram.cwl
in:
cram: bam_to_cram/cram
out:
[indexed_cram]