/
pvacseq.cwl
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pvacseq.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs"
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
inputs:
detect_variants_vcf:
type: File
sample_name:
type: string?
default: 'TUMOR'
normal_sample_name:
type: string?
default: 'NORMAL'
rnaseq_bam:
type: File
secondaryFiles: ['.bai']
reference_fasta:
type:
- string
- File
secondaryFiles: [.fai, ^.dict]
readcount_minimum_base_quality:
type: int?
readcount_minimum_mapping_quality:
type: int?
gene_expression_file:
type: File
transcript_expression_file:
type: File
expression_tool:
type: string?
default: 'kallisto'
alleles:
type: string[]
prediction_algorithms:
type: string[]
epitope_lengths:
type: int[]?
binding_threshold:
type: int?
allele_specific_binding_thresholds:
type: boolean?
minimum_fold_change:
type: float?
peptide_sequence_length:
type: int?
top_score_metric:
type:
- "null"
- type: enum
symbols: ["lowest", "median"]
additional_report_columns:
type:
- "null"
- type: enum
symbols: ["sample_name"]
fasta_size:
type: int?
downstream_sequence_length:
type: string?
exclude_nas:
type: boolean?
phased_proximal_variants_vcf:
type: File?
secondaryFiles: ['.tbi']
maximum_transcript_support_level:
type:
- "null"
- type: enum
symbols: ["1", "2", "3", "4", "5"]
normal_cov:
type: int?
tdna_cov:
type: int?
trna_cov:
type: int?
normal_vaf:
type: float?
tdna_vaf:
type: float?
trna_vaf:
type: float?
expn_val:
type: float?
net_chop_method:
type:
- "null"
- type: enum
symbols: ["cterm", "20s"]
net_chop_threshold:
type: float?
netmhc_stab:
type: boolean?
n_threads:
type: int?
variants_to_table_fields:
type: string[]?
default: [CHROM,POS,ID,REF,ALT]
variants_to_table_genotype_fields:
type: string[]?
default: [GT,AD,AF,DP,RAD,RAF,RDP,GX,TX]
vep_to_table_fields:
type: string[]?
default: [HGVSc,HGVSp]
outputs:
annotated_vcf:
type: File
outputSource: add_transcript_expression_data_to_vcf/annotated_expression_vcf
annotated_tsv:
type: File
outputSource: add_vep_fields_to_table/annotated_variants_tsv
pvacseq_predictions:
type: Directory
outputSource: pvacseq/pvacseq_predictions
steps:
tumor_rna_bam_readcount:
run: bam_readcount.cwl
in:
vcf: detect_variants_vcf
sample: sample_name
reference_fasta: reference_fasta
bam: rnaseq_bam
min_base_quality: readcount_minimum_base_quality
min_mapping_quality: readcount_minimum_mapping_quality
out:
[snv_bam_readcount_tsv, indel_bam_readcount_tsv, normalized_vcf]
add_tumor_rna_bam_readcount_to_vcf:
run: vcf_readcount_annotator.cwl
in:
vcf: tumor_rna_bam_readcount/normalized_vcf
snv_bam_readcount_tsv: tumor_rna_bam_readcount/snv_bam_readcount_tsv
indel_bam_readcount_tsv: tumor_rna_bam_readcount/indel_bam_readcount_tsv
data_type:
default: 'RNA'
sample_name: sample_name
out:
[annotated_bam_readcount_vcf]
add_gene_expression_data_to_vcf:
run: ../tools/vcf_expression_annotator.cwl
in:
vcf: add_tumor_rna_bam_readcount_to_vcf/annotated_bam_readcount_vcf
expression_file: gene_expression_file
expression_tool: expression_tool
data_type:
default: 'gene'
sample_name: sample_name
out:
[annotated_expression_vcf]
add_transcript_expression_data_to_vcf:
run: ../tools/vcf_expression_annotator.cwl
in:
vcf: add_gene_expression_data_to_vcf/annotated_expression_vcf
expression_file: transcript_expression_file
expression_tool: expression_tool
data_type:
default: 'transcript'
sample_name: sample_name
out:
[annotated_expression_vcf]
index:
run: ../tools/index_vcf.cwl
in:
vcf: add_transcript_expression_data_to_vcf/annotated_expression_vcf
out:
[indexed_vcf]
pvacseq:
run: ../tools/pvacseq.cwl
in:
input_vcf: index/indexed_vcf
sample_name: sample_name
alleles: alleles
prediction_algorithms: prediction_algorithms
epitope_lengths: epitope_lengths
normal_sample_name: normal_sample_name
minimum_fold_change: minimum_fold_change
peptide_sequence_length: peptide_sequence_length
top_score_metric: top_score_metric
additional_report_columns: additional_report_columns
fasta_size: fasta_size
downstream_sequence_length: downstream_sequence_length
exclude_nas: exclude_nas
phased_proximal_variants_vcf: phased_proximal_variants_vcf
maximum_transcript_support_level: maximum_transcript_support_level
normal_cov: normal_cov
tdna_cov: tdna_cov
trna_cov: trna_cov
normal_vaf: normal_vaf
tdna_vaf: tdna_vaf
trna_vaf: trna_vaf
expn_val: expn_val
net_chop_method: net_chop_method
net_chop_threshold: net_chop_threshold
netmhc_stab: netmhc_stab
n_threads: n_threads
out:
[pvacseq_predictions]
variants_to_table:
run: ../tools/variants_to_table.cwl
in:
reference: reference_fasta
vcf: index/indexed_vcf
fields: variants_to_table_fields
genotype_fields: variants_to_table_genotype_fields
out:
[variants_tsv]
add_vep_fields_to_table:
run: ../tools/add_vep_fields_to_table.cwl
in:
vcf: index/indexed_vcf
vep_fields: vep_to_table_fields
tsv: variants_to_table/variants_tsv
prefix:
default: 'pvacseq'
out: [annotated_variants_tsv]