Workflow to run pVACseq from detect_variants and rnaseq pipeline outputs

This workflow is Open Source and may be reused according to the terms of: MIT License

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
alleles	String[]
expn_val	Float (Optional)
tdna_cov	Integer (Optional)
tdna_vaf	Float (Optional)
trna_cov	Integer (Optional)
trna_vaf	Float (Optional)
n_threads	Integer (Optional)
fasta_size	Integer (Optional)
normal_cov	Integer (Optional)
normal_vaf	Float (Optional)
rnaseq_bam	File
exclude_nas	Boolean (Optional)
netmhc_stab	Boolean (Optional)
sample_name	String (Optional)
epitope_lengths	Integer[] (Optional)
expression_tool	String (Optional)
net_chop_method
reference_fasta	File
top_score_metric
binding_threshold	Integer (Optional)
net_chop_threshold	Float (Optional)
normal_sample_name	String (Optional)
detect_variants_vcf	File
minimum_fold_change	Float (Optional)
vep_to_table_fields	String[] (Optional)
gene_expression_file	File
prediction_algorithms	String[]
peptide_sequence_length	Integer (Optional)
variants_to_table_fields	String[] (Optional)
additional_report_columns
downstream_sequence_length	String (Optional)
transcript_expression_file	File
phased_proximal_variants_vcf	File (Optional)
readcount_minimum_base_quality	Integer (Optional)
maximum_transcript_support_level
readcount_minimum_mapping_quality	Integer (Optional)
variants_to_table_genotype_fields	String[] (Optional)
allele_specific_binding_thresholds	Boolean (Optional)

ID	Runs	Label
index	../tools/index_vcf.cwl (CommandLineTool)	vcf index
pvacseq	../tools/pvacseq.cwl (CommandLineTool)	run pVACseq
variants_to_table	../tools/variants_to_table.cwl (CommandLineTool)	SelectVariants (GATK 3.6)
add_vep_fields_to_table	../tools/add_vep_fields_to_table.cwl (CommandLineTool)	add VEP annotation to report
tumor_rna_bam_readcount	bam_readcount.cwl (Workflow)	bam_readcount workflow
add_gene_expression_data_to_vcf	../tools/vcf_expression_annotator.cwl (CommandLineTool)	add expression info to vcf
add_tumor_rna_bam_readcount_to_vcf	vcf_readcount_annotator.cwl (Workflow)	Add snv and indel bam-readcount files to a vcf
add_transcript_expression_data_to_vcf	../tools/vcf_expression_annotator.cwl (CommandLineTool)	add expression info to vcf

ID	Type	Label	Doc
annotated_tsv	File
annotated_vcf	File
pvacseq_predictions	Directory