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Updates to immuno workflow for upcoming 4.0.0 release #1085

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Updates to immuno workflow for upcoming 4.0.0 release #1085

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c9d3e31
Add new parameters for pVACseq for upcoming 4.0.0 release
susannasiebert Mar 10, 2023
324afc8
Add new parameters for pVACfuse for upcoming 4.0.0 release
susannasiebert Mar 10, 2023
abd6b04
Fix errors
susannasiebert Mar 10, 2023
2b4a147
Convert problematic_amino_acids input to string array
susannasiebert Mar 13, 2023
7183252
Update to latest docker image
susannasiebert Mar 15, 2023
5539546
Update to latest release candidate docker image
susannasiebert Mar 20, 2023
0d6bea2
Add ensembl version to reference fasta
susannasiebert Apr 5, 2023
dd4de17
Make peptide fasta an input
susannasiebert Apr 6, 2023
fbe0441
Update to release candidate v19
susannasiebert May 31, 2023
bd72727
Upgrade to official 4.0.0 release
susannasiebert Jun 21, 2023
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32 changes: 22 additions & 10 deletions definitions/pipelines/immuno.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -374,13 +374,17 @@ inputs:
type: int?
allele_specific_binding_thresholds:
type: boolean?
aggregate_inclusion_binding_threshold:
type: int?
minimum_fold_change:
type: float?
top_score_metric:
type:
- "null"
- type: enum
symbols: ["lowest", "median"]
problematic_amino_acids:
type: string?
additional_report_columns:
type:
- "null"
Expand All @@ -403,6 +407,10 @@ inputs:
- "null"
- type: enum
symbols: ["1", "2", "3", "4", "5"]
allele_specific_anchors:
type: boolean?
anchor_contribution_threshold:
type: float?
normal_cov:
type: int?
tdna_cov:
Expand Down Expand Up @@ -442,14 +450,6 @@ inputs:
label: "run_reference_proteome_similarity: sets an option whether to run reference proteome similarity or not"
doc: |
run_reference_proteome_similarity sets an option that decides whether it will run reference proteome similarity after all filtering and BLAST peptide sequences against the reference proteome to see if they appear elsewhere in the proteome.
blastp_db:
type:
- "null"
- type: enum
symbols: ["refseq_select_prot", "refseq_protein"]
label: "blastp_db: sets the reference proteome database to use with BLASTp"
doc: |
blastp_db sets the reference proteome database to use with BLASTp when enabling run_reference_proteome_similarity
pvacseq_threads:
type: int?
label: "pvacseq_threads: Number of threads to use for parallelizing pvacseq prediction"
Expand All @@ -473,6 +473,10 @@ inputs:
type: int?
pvacfuse_keep_tmp_files:
type: boolean?
pvacfuse_read_support:
type: int?
pvacfuse_expn_val:
type: float?

#FDA metrics inputs
reference_genome_name:
Expand Down Expand Up @@ -1278,12 +1282,15 @@ steps:
net_chop_threshold: net_chop_threshold
netmhc_stab: netmhc_stab
run_reference_proteome_similarity: run_reference_proteome_similarity
blastp_db: blastp_db
n_threads: pvacseq_threads
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
tumor_purity: tumor_purity
aggregate_inclusion_binding_threshold: aggregate_inclusion_binding_threshold
problematic_amino_acids: problematic_amino_acids
allele_specific_anchors: allele_specific_anchors
anchor_contribution_threshold: anchor_contribution_threshold
out:
[annotated_vcf, annotated_tsv, pvacseq_predictions]

Expand All @@ -1305,11 +1312,16 @@ steps:
top_score_metric: top_score_metric
net_chop_threshold: net_chop_threshold
run_reference_proteome_similarity: run_reference_proteome_similarity
blastp_db: blastp_db
additional_report_columns: additional_report_columns
fasta_size: fasta_size
downstream_sequence_length: downstream_sequence_length
exclude_nas: exclude_nas
n_threads: pvacseq_threads
star_fusion_file: rnaseq/star_fusion_abridge
read_support: pvacfuse_read_support
expn_val: pvacfuse_expn_val
allele_specific_binding_thresholds: allele_specific_binding_thresholds
aggregate_inclusion_binding_threshold: aggregate_inclusion_binding_threshold
problematic_amino_acids: problematic_amino_acids
out:
[pvacfuse_predictions]
18 changes: 12 additions & 6 deletions definitions/subworkflows/pvacseq.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,6 @@ inputs:
type: string[]
prediction_algorithms:
type: string[]
blastp_db:
type:
- "null"
- type: enum
symbols: ["refseq_select_prot", "refseq_protein"]
epitope_lengths_class_i:
type: int[]?
epitope_lengths_class_ii:
Expand All @@ -53,6 +48,8 @@ inputs:
type: int?
allele_specific_binding_thresholds:
type: boolean?
aggregate_inclusion_binding_threshold:
type: int?
minimum_fold_change:
type: float?
peptide_sequence_length:
Expand All @@ -62,6 +59,8 @@ inputs:
- "null"
- type: enum
symbols: ["lowest", "median"]
problematic_amino_acids:
type: string?
additional_report_columns:
type:
- "null"
Expand All @@ -81,6 +80,10 @@ inputs:
- "null"
- type: enum
symbols: ["1", "2", "3", "4", "5"]
allele_specific_anchors:
type: boolean?
anchor_contribution_threshold:
type: float?
normal_cov:
type: int?
tdna_cov:
Expand Down Expand Up @@ -211,9 +214,12 @@ steps:
net_chop_threshold: net_chop_threshold
netmhc_stab: netmhc_stab
run_reference_proteome_similarity: run_reference_proteome_similarity
blastp_db: blastp_db
n_threads: n_threads
tumor_purity: tumor_purity
aggregate_inclusion_binding_threshold: aggregate_inclusion_binding_threshold
problematic_amino_acids: problematic_amino_acids
allele_specific_anchors: allele_specific_anchors
anchor_contribution_threshold: anchor_contribution_threshold
out:
[pvacseq_predictions]
variants_to_table:
Expand Down
33 changes: 26 additions & 7 deletions definitions/tools/pvacfuse.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -16,13 +16,13 @@ arguments: [
"/usr/local/bin/pvacfuse",
"run",
"--iedb-install-directory", "/opt/iedb",
"--blastp-path", "/opt/ncbi-blast-2.12.0+/bin/blastp",
"--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.pep.all.fa.gz",
{ position: 5, valueFrom: "pvacfuse_predictions" },
]
requirements:
- class: ShellCommandRequirement
- class: DockerRequirement
dockerPull: "griffithlab/pvactools:3.1.1"
dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v3" #TODO: replace with final release version
- class: ResourceRequirement
ramMin: 16000
coresMin: $(inputs.n_threads)
Expand Down Expand Up @@ -66,6 +66,14 @@ inputs:
type: int?
inputBinding:
prefix: "--percentile-threshold"
allele_specific_binding_threshold:
type: boolean?
inputBinding:
prefix: "--allele-specific-binding-thresholds"
aggregate_inclusion_binding_threshold:
type: int?
inputBinding:
prefix: "--aggregate-inclusion-binding-threshold"
iedb_retries:
type: int?
inputBinding:
Expand All @@ -92,6 +100,10 @@ inputs:
symbols: ["lowest", "median"]
inputBinding:
prefix: "-m"
problematic_amino_acids:
type: string?
inputBinding:
prefix: "--problematic-amino-acids"
net_chop_threshold:
type: float?
inputBinding:
Expand All @@ -100,11 +112,6 @@ inputs:
type: boolean?
inputBinding:
prefix: "--run-reference-proteome-similarity"
blastp_db:
type:
- "null"
- type: enum
symbols: ["refseq_select_prot", "refseq_protein"]
additional_report_columns:
type:
- "null"
Expand All @@ -129,6 +136,18 @@ inputs:
inputBinding:
prefix: "--n-threads"
default: 8
star_fusion_file:
type: File?
inputBinding:
prefix: "--starfusion-file"
read_support:
type: int?
inputBinding:
prefix: "--read-support"
expn_val:
type: float?
inputBinding:
prefix: "--expn-val"
outputs:
mhc_i_all_epitopes:
type: File?
Expand Down
25 changes: 18 additions & 7 deletions definitions/tools/pvacseq.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -15,14 +15,14 @@ arguments: [
{ valueFrom: " && ", shellQuote: false },
"/usr/local/bin/pvacseq", "run",
"--iedb-install-directory", "/opt/iedb",
"--blastp-path", "/opt/ncbi-blast-2.12.0+/bin/blastp",
"--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.pep.all.fa.gz",
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Would it make sense for this to be an input the user could specify but with this path as the default?

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Good question. @malachig @chrisamiller do you have any opinions?

"--pass-only",
{ position: 5, valueFrom: "pvacseq_predictions" },
]
requirements:
- class: ShellCommandRequirement
- class: DockerRequirement
dockerPull: "griffithlab/pvactools:3.1.1"
dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v3" #TODO: replace with final release version
- class: ResourceRequirement
ramMin: 16000
coresMin: $(inputs.n_threads)
Expand Down Expand Up @@ -69,6 +69,10 @@ inputs:
type: boolean?
inputBinding:
prefix: "--allele-specific-binding-thresholds"
aggregate_inclusion_binding_threshold:
type: int?
inputBinding:
prefix: "--aggregate-inclusion-binding-threshold"
iedb_retries:
type: int?
inputBinding:
Expand Down Expand Up @@ -96,18 +100,17 @@ inputs:
type: boolean?
inputBinding:
prefix: "--run-reference-proteome-similarity"
blastp_db:
type:
- "null"
- type: enum
symbols: ["refseq_select_prot", "refseq_protein"]
top_score_metric:
type:
- "null"
- type: enum
symbols: ["lowest", "median"]
inputBinding:
prefix: "-m"
problematic_amino_acids:
type: string?
inputBinding:
prefix: "--problematic-amino-acids"
net_chop_threshold:
type: float?
inputBinding:
Expand Down Expand Up @@ -175,6 +178,14 @@ inputs:
symbols: ["1", "2", "3", "4", "5"]
inputBinding:
prefix: "--maximum-transcript-support-level"
allele_specific_anchors:
type: boolean?
inputBinding:
prefix: "--allele-specific-anchors"
anchor_contribution_threshold:
type: float?
inputBinding:
prefix: "--anchor-contribution-threshold"
tumor_purity:
type: float?
inputBinding:
Expand Down