diff --git a/definitions/immuno.wdl b/definitions/immuno.wdl index 7db3d30..df920ad 100644 --- a/definitions/immuno.wdl +++ b/definitions/immuno.wdl @@ -213,8 +213,11 @@ workflow immuno { Array[String]? clinical_mhc_classI_alleles Array[String]? clinical_mhc_classII_alleles - # --------- PVACseq Inputs ----------------------------------------- + # --------- HLA Consensus Inputs ----------------------------------- + String hla_source_mode + + # --------- PVACseq Inputs ----------------------------------------- Int? readcount_minimum_base_quality Int? readcount_minimum_mapping_quality Array[String] prediction_algorithms @@ -498,6 +501,7 @@ workflow immuno { run_reference_proteome_similarity=run_reference_proteome_similarity, peptide_fasta=peptide_fasta, n_threads=pvacseq_threads, + iedb_retries=iedb_retries, variants_to_table_fields=variants_to_table_fields, variants_to_table_genotype_fields=variants_to_table_genotype_fields, vep_to_table_fields=vep_to_table_fields, @@ -521,7 +525,6 @@ workflow immuno { epitope_lengths_class_ii=epitope_lengths_class_ii, binding_threshold=binding_threshold, percentile_threshold=percentile_threshold, - iedb_retries=iedb_retries, keep_tmp_files=pvacfuse_keep_tmp_files, net_chop_method=net_chop_method, netmhc_stab=netmhc_stab, @@ -534,6 +537,7 @@ workflow immuno { downstream_sequence_length=downstream_sequence_length, exclude_nas=exclude_nas, n_threads=pvacseq_threads, + iedb_retries=iedb_retries, read_support=pvacfuse_read_support, expn_val=pvacfuse_expn_val, allele_specific_binding_thresholds=allele_specific_binding_thresholds, diff --git a/definitions/subworkflows/pvacseq.wdl b/definitions/subworkflows/pvacseq.wdl index f67fd46..a819582 100644 --- a/definitions/subworkflows/pvacseq.wdl +++ b/definitions/subworkflows/pvacseq.wdl @@ -52,6 +52,7 @@ workflow pvacseq { Boolean? netmhc_stab Boolean? run_reference_proteome_similarity Int? n_threads + Int? iedb_retries Array[String] variants_to_table_fields = ["CHROM", "POS", "ID", "REF", "ALT"] Array[String] variants_to_table_genotype_fields = ["GT", "AD", "AF", "DP", "RAD", "RAF", "RDP", "GX", "TX"] Array[String] vep_to_table_fields = ["HGVSc", "HGVSp"] @@ -143,6 +144,7 @@ workflow pvacseq { run_reference_proteome_similarity=run_reference_proteome_similarity, peptide_fasta=peptide_fasta, n_threads=n_threads, + iedb_retries=iedb_retries, tumor_purity=tumor_purity, allele_specific_binding_thresholds=allele_specific_binding_thresholds, aggregate_inclusion_binding_threshold=aggregate_inclusion_binding_threshold,