subworkflows_pvacseq.cwl

Documentation for pvacseq.cwl

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Overview

Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

Inputs

Name	Label	Description	Type	Secondary Files
detect_variants_vcf			File
sample_name			string?
normal_sample_name			string?
rnaseq_bam			File	['.bai']
reference_fasta			['string', 'File']	['.fai', '^.dict']
readcount_minimum_base_quality			int?
readcount_minimum_mapping_quality			int?
gene_expression_file			File
transcript_expression_file			File
expression_tool			string?
alleles			string[]
prediction_algorithms			string[]
blastp_db			['null', {'type': 'enum', 'symbols': ['refseq_select_prot', 'refseq_protein']}]
epitope_lengths_class_i			int[]?
epitope_lengths_class_ii			int[]?
binding_threshold			int?
percentile_threshold			int?
allele_specific_binding_thresholds			boolean?
minimum_fold_change			float?
peptide_sequence_length			int?
top_score_metric			['null', {'type': 'enum', 'symbols': ['lowest', 'median']}]
additional_report_columns			['null', {'type': 'enum', 'symbols': ['sample_name']}]
fasta_size			int?
downstream_sequence_length			string?
exclude_nas			boolean?
phased_proximal_variants_vcf			File?	['.tbi']
maximum_transcript_support_level			['null', {'type': 'enum', 'symbols': ['1', '2', '3', '4', '5']}]
normal_cov			int?
tdna_cov			int?
trna_cov			int?
normal_vaf			float?
tdna_vaf			float?
trna_vaf			float?
expn_val			float?
net_chop_method			['null', {'type': 'enum', 'symbols': ['cterm', '20s']}]
net_chop_threshold			float?
netmhc_stab			boolean?
run_reference_proteome_similarity			boolean?
n_threads			int?
variants_to_table_fields			string[]?
variants_to_table_genotype_fields			string[]?
vep_to_table_fields			string[]?
tumor_purity			float?

Outputs

Name	Label	Description	Type	Secondary Files
annotated_vcf			File
annotated_tsv			File
pvacseq_predictions			Directory

Steps

Name	CWL Run
tumor_rna_bam_readcount	subworkflows/bam_readcount.cwl
add_tumor_rna_bam_readcount_to_vcf	subworkflows/vcf_readcount_annotator.cwl
add_gene_expression_data_to_vcf	tools/vcf_expression_annotator.cwl
add_transcript_expression_data_to_vcf	tools/vcf_expression_annotator.cwl
index	tools/index_vcf.cwl
pvacseq	tools/pvacseq.cwl
variants_to_table	tools/variants_to_table.cwl
add_vep_fields_to_table	tools/add_vep_fields_to_table.cwl