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germline_exome_hla_typing.cwl
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germline_exome_hla_typing.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "exome alignment and germline variant detection, with optitype for HLA typing"
requirements:
- class: SchemaDefRequirement
types:
- $import: ../types/labelled_file.yml
- $import: ../types/sequence_data.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[]
mills:
type: File
secondaryFiles: [.tbi]
known_indels:
type: File
secondaryFiles: [.tbi]
dbsnp_vcf:
type: File
secondaryFiles: [.tbi]
bqsr_intervals:
type: string[]?
bait_intervals:
type: File
target_intervals:
type: File
per_base_intervals:
type: ../types/labelled_file.yml#labelled_file[]
per_target_intervals:
type: ../types/labelled_file.yml#labelled_file[]
summary_intervals:
type: ../types/labelled_file.yml#labelled_file[]
omni_vcf:
type: File
secondaryFiles: [.tbi]
picard_metric_accumulation_level:
type: string
emit_reference_confidence:
type:
type: enum
symbols: ['NONE', 'BP_RESOLUTION', 'GVCF']
gvcf_gq_bands:
type: string[]
intervals:
type:
type: array
items:
type: array
items: string
ploidy:
type: int?
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_custom_annotations:
type: ../types/vep_custom_annotation.yml#vep_custom_annotation[]
doc: "custom type, check types directory for input format"
qc_minimum_mapping_quality:
type: int?
qc_minimum_base_quality:
type: int?
optitype_name:
type: string?
outputs:
cram:
type: File
outputSource: germline_exome/cram
mark_duplicates_metrics:
type: File
outputSource: germline_exome/mark_duplicates_metrics
insert_size_metrics:
type: File
outputSource: germline_exome/insert_size_metrics
insert_size_histogram:
type: File
outputSource: germline_exome/insert_size_histogram
alignment_summary_metrics:
type: File
outputSource: germline_exome/alignment_summary_metrics
hs_metrics:
type: File
outputSource: germline_exome/hs_metrics
per_target_coverage_metrics:
type: File[]
outputSource: germline_exome/per_target_coverage_metrics
per_target_hs_metrics:
type: File[]
outputSource: germline_exome/per_target_hs_metrics
per_base_coverage_metrics:
type: File[]
outputSource: germline_exome/per_base_coverage_metrics
per_base_hs_metrics:
type: File[]
outputSource: germline_exome/per_base_hs_metrics
summary_hs_metrics:
type: File[]
outputSource: germline_exome/summary_hs_metrics
flagstats:
type: File
outputSource: germline_exome/flagstats
verify_bam_id_metrics:
type: File
outputSource: germline_exome/verify_bam_id_metrics
verify_bam_id_depth:
type: File
outputSource: germline_exome/verify_bam_id_depth
gvcf:
type: File[]
outputSource: germline_exome/gvcf
raw_vcf:
type: File
outputSource: germline_exome/raw_vcf
secondaryFiles: [.tbi]
final_vcf:
type: File
outputSource: germline_exome/final_vcf
secondaryFiles: [.tbi]
filtered_vcf:
type: File
outputSource: germline_exome/filtered_vcf
secondaryFiles: [.tbi]
vep_summary:
type: File
outputSource: germline_exome/vep_summary
optitype_tsv:
type: File
outputSource: optitype/optitype_tsv
optitype_plot:
type: File
outputSource: optitype/optitype_plot
steps:
germline_exome:
run: germline_exome.cwl
in:
reference: reference
sequence: sequence
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
emit_reference_confidence: emit_reference_confidence
gvcf_gq_bands: gvcf_gq_bands
intervals: intervals
ploidy: ploidy
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_custom_annotations: vep_custom_annotations
qc_minimum_mapping_quality: qc_minimum_mapping_quality
qc_minimum_base_quality: qc_minimum_base_quality
out:
[cram, mark_duplicates_metrics, insert_size_metrics, insert_size_histogram, 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, gvcf, raw_vcf, final_vcf, filtered_vcf, vep_summary]
optitype:
run: ../tools/optitype_dna.cwl
in:
optitype_name: optitype_name
cram: germline_exome/cram
reference: reference
out:
[optitype_tsv, optitype_plot]