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Upgrade pvacseq.wdl and pvacfuse.wdl to work with pVACtools 5.0 #168

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Upgrade pvacseq.wdl and pvacfuse.wdl to work with pVACtools 5.0 #168

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7 changes: 6 additions & 1 deletion definitions/immuno.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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 {
Expand Down Expand Up @@ -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,
}

Expand Down
4 changes: 4 additions & 0 deletions definitions/subworkflows/pvacseq.wdl
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Expand Up @@ -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 {
Expand Down Expand Up @@ -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 {
Expand Down
4 changes: 3 additions & 1 deletion definitions/tools/pvacfuse.wdl
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Expand Up @@ -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
Expand All @@ -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"
Expand All @@ -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 ""} \
Expand Down
7 changes: 6 additions & 1 deletion definitions/tools/pvacseq.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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}
Expand All @@ -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 ""} \
Expand All @@ -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
Expand Down
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