subworkflows_pvacseq.cwl - genome/analysis-workflows GitHub Wiki
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