tools_pvacseq.cwl

Documentation for pvacseq.cwl

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Overview

run pVACseq

Docker Requirement

griffithlab/pvactools:3.1.1

Inputs

Name	Label	Description	Type	Secondary Files
input_vcf			File	['.tbi']
sample_name			string
alleles			string[]
prediction_algorithms			string[]
epitope_lengths_class_i			int[]?
epitope_lengths_class_ii			int[]?
binding_threshold			int?
percentile_threshold			int?
allele_specific_binding_thresholds			boolean?
iedb_retries			int?
keep_tmp_files			boolean?
normal_sample_name			string?
net_chop_method			['null', {'type': 'enum', 'symbols': ['cterm', '20s']}]
netmhc_stab			boolean?
run_reference_proteome_similarity			boolean?
blastp_db			['null', {'type': 'enum', 'symbols': ['refseq_select_prot', 'refseq_protein']}]
top_score_metric			['null', {'type': 'enum', 'symbols': ['lowest', 'median']}]
net_chop_threshold			float?
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']
minimum_fold_change			float?
normal_cov			int?
tdna_cov			int?
trna_cov			int?
normal_vaf			float?
tdna_vaf			float?
trna_vaf			float?
expn_val			float?
maximum_transcript_support_level			['null', {'type': 'enum', 'symbols': ['1', '2', '3', '4', '5']}]
tumor_purity			float?
n_threads			int?

Outputs

Name	Label	Description	Type	Secondary Files
mhc_i_all_epitopes			File?
mhc_i_aggregated_report			File?
mhc_i_aggregated_metrics_file			File?
mhc_i_filtered_epitopes			File?
mhc_ii_all_epitopes			File?
mhc_ii_aggregated_report			File?
mhc_ii_aggregated_metrics_file			File?
mhc_ii_filtered_epitopes			File?
combined_all_epitopes			File?
combined_aggregated_report			File?
combined_aggregated_metrics_file			File?
combined_filtered_epitopes			File?
pvacseq_predictions			Directory