diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl index 33fda187..e0c14b70 100644 --- a/definitions/pipelines/immuno.cwl +++ b/definitions/pipelines/immuno.cwl @@ -374,6 +374,8 @@ inputs: type: int? allele_specific_binding_thresholds: type: boolean? + aggregate_inclusion_binding_threshold: + type: int? minimum_fold_change: type: float? top_score_metric: @@ -381,6 +383,8 @@ inputs: - "null" - type: enum symbols: ["lowest", "median"] + problematic_amino_acids: + type: string[]? additional_report_columns: type: - "null" @@ -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: @@ -442,14 +450,11 @@ 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" + peptide_fasta: + type: File? + label: "run_reference_proteome_similarity: sets an option whether to run reference proteome similarity or not" doc: | - blastp_db sets the reference proteome database to use with BLASTp when enabling run_reference_proteome_similarity + peptide_fasta is a path to a reference proteome fasta file to use when running reference proteome similarity. pvacseq_threads: type: int? label: "pvacseq_threads: Number of threads to use for parallelizing pvacseq prediction" @@ -473,6 +478,10 @@ 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: @@ -1278,12 +1287,16 @@ steps: net_chop_threshold: net_chop_threshold netmhc_stab: netmhc_stab run_reference_proteome_similarity: run_reference_proteome_similarity - blastp_db: blastp_db + peptide_fasta: peptide_fasta 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] @@ -1305,11 +1318,17 @@ 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 + peptide_fasta: peptide_fasta 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] diff --git a/definitions/subworkflows/pvacseq.cwl b/definitions/subworkflows/pvacseq.cwl index 260911b8..3040c707 100644 --- a/definitions/subworkflows/pvacseq.cwl +++ b/definitions/subworkflows/pvacseq.cwl @@ -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: @@ -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: @@ -62,6 +59,8 @@ inputs: - "null" - type: enum symbols: ["lowest", "median"] + problematic_amino_acids: + type: string[]? additional_report_columns: type: - "null" @@ -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: @@ -106,6 +109,8 @@ inputs: type: boolean? run_reference_proteome_similarity: type: boolean? + peptide_fasta: + type: File? n_threads: type: int? variants_to_table_fields: @@ -211,9 +216,13 @@ steps: net_chop_threshold: net_chop_threshold netmhc_stab: netmhc_stab run_reference_proteome_similarity: run_reference_proteome_similarity - blastp_db: blastp_db + peptide_fasta: peptide_fasta 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: diff --git a/definitions/tools/pvacbind.cwl b/definitions/tools/pvacbind.cwl index 56a3774c..8c80279f 100644 --- a/definitions/tools/pvacbind.cwl +++ b/definitions/tools/pvacbind.cwl @@ -15,13 +15,13 @@ arguments: [ { valueFrom: " && ", shellQuote: false }, "/usr/local/bin/pvacbind", "run", "--iedb-install-directory", "/opt/iedb", - "--blastp-path", "/opt/ncbi-blast-2.12.0+/bin/blastp", + "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.101.pep.all.fa.gz", { position: 5, valueFrom: $(runtime.outdir) }, ] requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "griffithlab/pvactools:3.1.1" + dockerPull: "griffithlab/pvactools:4.0.0" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) @@ -101,11 +101,6 @@ 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" diff --git a/definitions/tools/pvacfuse.cwl b/definitions/tools/pvacfuse.cwl index f4cd15a7..631fe693 100644 --- a/definitions/tools/pvacfuse.cwl +++ b/definitions/tools/pvacfuse.cwl @@ -16,13 +16,12 @@ arguments: [ "/usr/local/bin/pvacfuse", "run", "--iedb-install-directory", "/opt/iedb", - "--blastp-path", "/opt/ncbi-blast-2.12.0+/bin/blastp", { position: 5, valueFrom: "pvacfuse_predictions" }, ] requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "griffithlab/pvactools:3.1.1" + dockerPull: "griffithlab/pvactools:4.0.0" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) @@ -66,6 +65,14 @@ 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: @@ -92,6 +99,11 @@ inputs: symbols: ["lowest", "median"] inputBinding: prefix: "-m" + problematic_amino_acids: + type: string[]? + inputBinding: + prefix: "--problematic-amino-acids" + itemSeparator: ',' net_chop_threshold: type: float? inputBinding: @@ -100,11 +112,10 @@ inputs: type: boolean? inputBinding: prefix: "--run-reference-proteome-similarity" - blastp_db: - type: - - "null" - - type: enum - symbols: ["refseq_select_prot", "refseq_protein"] + peptide_fasta: + type: File? + inputBinding: + prefix: "--peptide-fasta" additional_report_columns: type: - "null" @@ -129,6 +140,18 @@ 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? diff --git a/definitions/tools/pvacseq.cwl b/definitions/tools/pvacseq.cwl index 6de65f48..2ad53bae 100644 --- a/definitions/tools/pvacseq.cwl +++ b/definitions/tools/pvacseq.cwl @@ -15,14 +15,13 @@ arguments: [ { valueFrom: " && ", shellQuote: false }, "/usr/local/bin/pvacseq", "run", "--iedb-install-directory", "/opt/iedb", - "--blastp-path", "/opt/ncbi-blast-2.12.0+/bin/blastp", "--pass-only", { position: 5, valueFrom: "pvacseq_predictions" }, ] requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "griffithlab/pvactools:3.1.1" + dockerPull: "griffithlab/pvactools:4.0.0" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) @@ -69,6 +68,10 @@ 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: @@ -96,11 +99,10 @@ inputs: type: boolean? inputBinding: prefix: "--run-reference-proteome-similarity" - blastp_db: - type: - - "null" - - type: enum - symbols: ["refseq_select_prot", "refseq_protein"] + peptide_fasta: + type: File? + inputBinding: + prefix: "--peptide-fasta" top_score_metric: type: - "null" @@ -108,6 +110,11 @@ inputs: symbols: ["lowest", "median"] inputBinding: prefix: "-m" + problematic_amino_acids: + type: string[]? + inputBinding: + prefix: "--problematic-amino-acids" + itemSeparator: ',' net_chop_threshold: type: float? inputBinding: @@ -175,6 +182,14 @@ 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: diff --git a/definitions/tools/pvacvector.cwl b/definitions/tools/pvacvector.cwl index feba6658..c507ade9 100644 --- a/definitions/tools/pvacvector.cwl +++ b/definitions/tools/pvacvector.cwl @@ -16,13 +16,12 @@ arguments: [ "/usr/local/bin/pvacvector", "run", "--iedb-install-directory", "/opt/iedb", - "--blastp-path", "/opt/ncbi-blast-2.12.0+/bin/blastp", { position: 5, valueFrom: $(runtime.outdir) }, ] requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "griffithlab/pvactools:3.1.1" + dockerPull: "griffithlab/pvactools:4.0.0" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads)