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clarify two immuno inputs #167

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Dec 26, 2024
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Merged

clarify two immuno inputs #167

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8 changes: 6 additions & 2 deletions definitions/immuno.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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,
Expand All @@ -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,
Expand All @@ -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,
Expand Down
2 changes: 2 additions & 0 deletions definitions/subworkflows/pvacseq.wdl
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Expand Up @@ -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"]
Expand Down Expand Up @@ -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,
Expand Down
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