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	Integer (Optional)
tdna_cov	Integer (Optional)
tdna_vaf	Float (Optional)
trna_cov	Integer (Optional)
trna_vaf	Float (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	String
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)
gene_expression_file	File
prediction_algorithms	String[]
peptide_sequence_length	Integer (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)
allele_specific_binding_thresholds	Boolean (Optional)

ID	Runs	Label
pvacseq	../tools/pvacseq.cwl (CommandLineTool)	run pVACseq
tumor_rna_bam_readcount	../tools/bam_readcount.cwl (CommandLineTool)	run bam-readcount
add_gene_expression_data_to_vcf	../tools/vcf_expression_annotator.cwl (CommandLineTool)	add expression info to vcf
add_tumor_rna_bam_readcount_to_vcf	../tools/vcf_readcount_annotator.cwl (CommandLineTool)	add bam_readcount info to vcf
add_transcript_expression_data_to_vcf	../tools/vcf_expression_annotator.cwl (CommandLineTool)	add expression info to vcf

ID	Type	Label	Doc
mhc_i_all_epitopes	File (Optional)
mhc_ii_all_epitopes	File (Optional)
combined_all_epitopes	File (Optional)
mhc_i_ranked_epitopes	File (Optional)
mhc_ii_ranked_epitopes	File (Optional)
mhc_i_filtered_epitopes	File (Optional)
combined_ranked_epitopes	File (Optional)
mhc_ii_filtered_epitopes	File (Optional)
combined_filtered_epitopes	File (Optional)