Upgrade pvacseq.wdl and pvacfuse.wdl to work with pVACtools 5.0

wustl-oncology · Dec 19, 2024 · 7bc2199 · 7bc2199
1 parent de14a42
commit 7bc2199
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Showing 4 changed files with 19 additions and 3 deletions.
diff --git a/definitions/immuno.wdl b/definitions/immuno.wdl
@@ -247,11 +247,13 @@ workflow immuno {
     Float? tumor_purity
     Boolean? allele_specific_binding_thresholds
     Int? aggregate_inclusion_binding_threshold
+    Int? aggregate_inclusion_count_limit
     Array[String]? problematic_amino_acids
     Boolean? allele_specific_anchors
     Float? anchor_contribution_threshold
     Int? pvacfuse_read_support
     Float? pvacfuse_expn_val
+    Array[String]? biotypes
 
     # --------- FDA metrics inputs -------------------------------------
     String? reference_genome_name
@@ -505,9 +507,11 @@ workflow immuno {
     tumor_purity=tumor_purity,
     allele_specific_binding_thresholds=allele_specific_binding_thresholds,
     aggregate_inclusion_binding_threshold=aggregate_inclusion_binding_threshold,
+    aggregate_inclusion_count_limit=aggregate_inclusion_count_limit,
     problematic_amino_acids=problematic_amino_acids,
     allele_specific_anchors=allele_specific_anchors,
-    anchor_contribution_threshold=anchor_contribution_threshold
+    anchor_contribution_threshold=anchor_contribution_threshold,
+    biotypes=biotypes
   }
 
   call pf.pvacfuse {
@@ -538,6 +542,7 @@ workflow immuno {
     expn_val=pvacfuse_expn_val,
     allele_specific_binding_thresholds=allele_specific_binding_thresholds,
     aggregate_inclusion_binding_threshold=aggregate_inclusion_binding_threshold,
+    aggregate_inclusion_count_limit=aggregate_inclusion_count_limit,
     problematic_amino_acids=problematic_amino_acids,
   }
 

diff --git a/definitions/subworkflows/pvacseq.wdl b/definitions/subworkflows/pvacseq.wdl
@@ -58,10 +58,12 @@ workflow pvacseq {
     Float? tumor_purity
     Boolean? allele_specific_binding_thresholds
     Int? aggregate_inclusion_binding_threshold
+    Int? aggregate_inclusion_count_limit
     Array[String]? problematic_amino_acids
     Boolean? allele_specific_anchors
     Float? anchor_contribution_threshold
     String? prefix = "pvacseq"
+    Array[String]? biotypes
   }
 
   call br.bamReadcount as tumorRnaBamReadcount {
@@ -146,9 +148,11 @@ workflow pvacseq {
     tumor_purity=tumor_purity,
     allele_specific_binding_thresholds=allele_specific_binding_thresholds,
     aggregate_inclusion_binding_threshold=aggregate_inclusion_binding_threshold,
+    aggregate_inclusion_count_limit=aggregate_inclusion_count_limit,
     problematic_amino_acids=problematic_amino_acids,
     allele_specific_anchors=allele_specific_anchors,
     anchor_contribution_threshold=anchor_contribution_threshold,
+    biotypes=biotypes
   }
 
   call vtt.variantsToTable {

diff --git a/definitions/tools/pvacfuse.wdl b/definitions/tools/pvacfuse.wdl
@@ -25,6 +25,7 @@ task pvacfuse {
     Int n_threads = 8
     Boolean allele_specific_binding_thresholds = false
     Int? aggregate_inclusion_binding_threshold
+    Int? aggregate_inclusion_count_limit
     Array[String]? problematic_amino_acids
     File? star_fusion_file
     Int? read_support
@@ -35,7 +36,7 @@ task pvacfuse {
   runtime {
     preemptible: 1
     maxRetries: 2
-    docker: "griffithlab/pvactools:4.4.1"
+    docker: "griffithlab/pvactools:5.0.1"
     memory: "32GB"
     cpu: n_threads
     disks: "local-disk ~{space_needed_gb} HDD"
@@ -60,6 +61,7 @@ task pvacfuse {
     ~{if defined(percentile_threshold) then "--percentile-threshold ~{percentile_threshold}" else ""} \
     ~{if allele_specific_binding_thresholds then "--allele-specific-binding-thresholds" else ""} \
     ~{if defined(aggregate_inclusion_binding_threshold) then "--aggregate-inclusion-binding-threshold ~{aggregate_inclusion_binding_threshold}" else ""} \
+    ~{if defined(aggregate_inclusion_count_limit) then "--aggregate-inclusion-count-limit ~{aggregate_inclusion_count_limit}" else ""} \
     ~{if defined(iedb_retries) then "-r ~{iedb_retries}" else ""} \
     ~{if keep_tmp_files then "-k" else ""} \
     ~{if defined(net_chop_method) then "--net-chop-method ~{net_chop_method}" else ""} \

diff --git a/definitions/tools/pvacseq.wdl b/definitions/tools/pvacseq.wdl
@@ -36,8 +36,10 @@ task pvacseq {
     Float? expn_val
     Int? maximum_transcript_support_level  # enum [1, 2, 3, 4, 5]
     Int? aggregate_inclusion_binding_threshold
+    Int? aggregate_inclusion_count_limit
     Array[String]? problematic_amino_acids
     Float? anchor_contribution_threshold
+    Array[String]? biotypes
 
     Boolean allele_specific_binding_thresholds = false
     Boolean keep_tmp_files = false
@@ -56,14 +58,15 @@ task pvacseq {
     maxRetries: 2
     memory: "32GB"
     cpu: n_threads
-    docker: "griffithlab/pvactools:4.4.1"
+    docker: "griffithlab/pvactools:5.0.1"
     disks: "local-disk ~{space_needed_gb} HDD"
   }
 
   # explicit typing required, don't inline
   Array[Int] epitope_i = select_first([epitope_lengths_class_i, []])
   Array[Int] epitope_ii = select_first([epitope_lengths_class_ii, []])
   Array[String] problematic_aa = select_first([problematic_amino_acids, []])
+  Array[String] biotypes_list = select_first([biotypes, []])
   command <<<
     # touch each tbi to ensure they have a timestamp after the vcf
     touch ~{phased_proximal_variants_vcf_tbi}
@@ -79,6 +82,7 @@ task pvacseq {
     ~{if defined(percentile_threshold) then "--percentile-threshold ~{percentile_threshold}" else ""} \
     ~{if allele_specific_binding_thresholds then "--allele-specific-binding-thresholds" else ""} \
     ~{if defined(aggregate_inclusion_binding_threshold) then "--aggregate-inclusion-binding-threshold ~{aggregate_inclusion_binding_threshold}" else ""} \
+    ~{if defined(aggregate_inclusion_count_limit) then "--aggregate-inclusion-count-limit ~{aggregate_inclusion_count_limit}" else ""} \
     ~{if defined(iedb_retries) then "-r ~{iedb_retries}" else ""} \
     ~{if keep_tmp_files then "-k" else ""} \
     ~{if defined(normal_sample_name) then "--normal-sample-name ~{normal_sample_name}" else ""} \
@@ -105,6 +109,7 @@ task pvacseq {
     ~{if length(problematic_aa) > 0 then "--problematic-amino-acids" else ""} ~{sep="," problematic_aa} \
     ~{if allele_specific_anchors then "--allele-specific-anchors" else ""} \
     ~{if defined(anchor_contribution_threshold) then "--anchor-contribution-threshold ~{anchor_contribution_threshold}" else ""} \
+    ~{if length(biotypes_list) > 0 then "--biotypes" else ""} ~{sep="," biotypes_list} \
     --n-threads ~{n_threads} \
     ~{input_vcf} ~{sample_name} ~{sep="," alleles} ~{sep=" " prediction_algorithms} \
     pvacseq_predictions