From c9d3e31dfd186038b86d857637220ad53438b547 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Fri, 10 Mar 2023 13:57:52 -0600 Subject: [PATCH 01/10] Add new parameters for pVACseq for upcoming 4.0.0 release --- definitions/pipelines/immuno.cwl | 21 ++++++++++++--------- definitions/subworkflows/pvacseq.cwl | 18 ++++++++++++------ definitions/tools/pvacseq.cwl | 25 ++++++++++++++++++------- 3 files changed, 42 insertions(+), 22 deletions(-) diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl index 33fda187..04c06d38 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 +450,6 @@ 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" @@ -1278,12 +1278,15 @@ 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] diff --git a/definitions/subworkflows/pvacseq.cwl b/definitions/subworkflows/pvacseq.cwl index 260911b8..a81227ee 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: @@ -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: diff --git a/definitions/tools/pvacseq.cwl b/definitions/tools/pvacseq.cwl index 6de65f48..ac81bad1 100644 --- a/definitions/tools/pvacseq.cwl +++ b/definitions/tools/pvacseq.cwl @@ -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", "--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) @@ -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: @@ -96,11 +100,6 @@ 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" @@ -108,6 +107,10 @@ inputs: symbols: ["lowest", "median"] inputBinding: prefix: "-m" + problematic_amino_acids: + type: string? + inputBinding: + prefix: "--problematic-amino-acids" net_chop_threshold: type: float? inputBinding: @@ -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: From 324afc8a9e7844c8684a5ba0fb66a04b67daa74b Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Fri, 10 Mar 2023 13:58:13 -0600 Subject: [PATCH 02/10] Add new parameters for pVACfuse for upcoming 4.0.0 release --- definitions/pipelines/immuno.cwl | 11 ++++++++++- definitions/tools/pvacfuse.cwl | 33 +++++++++++++++++++++++++------- 2 files changed, 36 insertions(+), 8 deletions(-) diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl index 04c06d38..e3678b8f 100644 --- a/definitions/pipelines/immuno.cwl +++ b/definitions/pipelines/immuno.cwl @@ -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: @@ -1308,11 +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_threshold: allele_specific_binding_threshold + aggregate_inclusion_binding_threshold: aggregate_inclusion_binding_threshold + problematic_amino_acids: problematic_amino_acids out: [pvacfuse_predictions] diff --git a/definitions/tools/pvacfuse.cwl b/definitions/tools/pvacfuse.cwl index f4cd15a7..559fd0de 100644 --- a/definitions/tools/pvacfuse.cwl +++ b/definitions/tools/pvacfuse.cwl @@ -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) @@ -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: @@ -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: @@ -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" @@ -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? From abd6b04a98a8718e3b5d1b0a1462948d0b5b11e6 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Fri, 10 Mar 2023 14:33:44 -0600 Subject: [PATCH 03/10] Fix errors --- definitions/pipelines/immuno.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl index e3678b8f..799badd6 100644 --- a/definitions/pipelines/immuno.cwl +++ b/definitions/pipelines/immuno.cwl @@ -1320,7 +1320,7 @@ steps: star_fusion_file: rnaseq/star_fusion_abridge read_support: pvacfuse_read_support expn_val: pvacfuse_expn_val - allele_specific_binding_threshold: allele_specific_binding_threshold + allele_specific_binding_thresholds: allele_specific_binding_thresholds aggregate_inclusion_binding_threshold: aggregate_inclusion_binding_threshold problematic_amino_acids: problematic_amino_acids out: From 2b4a147b705162f87fe897a766d5edda01f326ea Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Mon, 13 Mar 2023 13:33:44 -0500 Subject: [PATCH 04/10] Convert problematic_amino_acids input to string array --- definitions/pipelines/immuno.cwl | 2 +- definitions/subworkflows/pvacseq.cwl | 2 +- definitions/tools/pvacfuse.cwl | 3 ++- definitions/tools/pvacseq.cwl | 3 ++- 4 files changed, 6 insertions(+), 4 deletions(-) diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl index 799badd6..b2d80278 100644 --- a/definitions/pipelines/immuno.cwl +++ b/definitions/pipelines/immuno.cwl @@ -384,7 +384,7 @@ inputs: - type: enum symbols: ["lowest", "median"] problematic_amino_acids: - type: string? + type: string[]? additional_report_columns: type: - "null" diff --git a/definitions/subworkflows/pvacseq.cwl b/definitions/subworkflows/pvacseq.cwl index a81227ee..9ba3e257 100644 --- a/definitions/subworkflows/pvacseq.cwl +++ b/definitions/subworkflows/pvacseq.cwl @@ -60,7 +60,7 @@ inputs: - type: enum symbols: ["lowest", "median"] problematic_amino_acids: - type: string? + type: string[]? additional_report_columns: type: - "null" diff --git a/definitions/tools/pvacfuse.cwl b/definitions/tools/pvacfuse.cwl index 559fd0de..986af365 100644 --- a/definitions/tools/pvacfuse.cwl +++ b/definitions/tools/pvacfuse.cwl @@ -101,9 +101,10 @@ inputs: inputBinding: prefix: "-m" problematic_amino_acids: - type: string? + type: string[]? inputBinding: prefix: "--problematic-amino-acids" + itemSeparator: ',' net_chop_threshold: type: float? inputBinding: diff --git a/definitions/tools/pvacseq.cwl b/definitions/tools/pvacseq.cwl index ac81bad1..23e33c88 100644 --- a/definitions/tools/pvacseq.cwl +++ b/definitions/tools/pvacseq.cwl @@ -108,9 +108,10 @@ inputs: inputBinding: prefix: "-m" problematic_amino_acids: - type: string? + type: string[]? inputBinding: prefix: "--problematic-amino-acids" + itemSeparator: ',' net_chop_threshold: type: float? inputBinding: From 718325225a4e17cc7752f2d2e141cb96ad142965 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 15 Mar 2023 10:29:39 -0500 Subject: [PATCH 05/10] Update to latest docker image --- definitions/tools/pvacbind.cwl | 9 ++------- definitions/tools/pvacfuse.cwl | 2 +- definitions/tools/pvacseq.cwl | 2 +- definitions/tools/pvacvector.cwl | 3 +-- 4 files changed, 5 insertions(+), 11 deletions(-) diff --git a/definitions/tools/pvacbind.cwl b/definitions/tools/pvacbind.cwl index 56a3774c..23cb9a0f 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.pep.all.fa.gz", { position: 5, valueFrom: $(runtime.outdir) }, ] requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "griffithlab/pvactools:3.1.1" + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v4" - 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 986af365..52594036 100644 --- a/definitions/tools/pvacfuse.cwl +++ b/definitions/tools/pvacfuse.cwl @@ -22,7 +22,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v3" #TODO: replace with final release version + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v4" #TODO: replace with final release version - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacseq.cwl b/definitions/tools/pvacseq.cwl index 23e33c88..2203c490 100644 --- a/definitions/tools/pvacseq.cwl +++ b/definitions/tools/pvacseq.cwl @@ -22,7 +22,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v3" #TODO: replace with final release version + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v4" #TODO: replace with final release version - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacvector.cwl b/definitions/tools/pvacvector.cwl index feba6658..41712848 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: "susannakiwala/pvactools:4.0.0_rc_pvacview_v4" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) From 55395461b0de66b76ad7ced843b2c0e717e66626 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Mon, 20 Mar 2023 18:04:05 -0500 Subject: [PATCH 06/10] Update to latest release candidate docker image --- definitions/tools/pvacbind.cwl | 2 +- definitions/tools/pvacfuse.cwl | 2 +- definitions/tools/pvacseq.cwl | 2 +- definitions/tools/pvacvector.cwl | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/definitions/tools/pvacbind.cwl b/definitions/tools/pvacbind.cwl index 23cb9a0f..fec458f4 100644 --- a/definitions/tools/pvacbind.cwl +++ b/definitions/tools/pvacbind.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v4" + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v5" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacfuse.cwl b/definitions/tools/pvacfuse.cwl index 52594036..d6083917 100644 --- a/definitions/tools/pvacfuse.cwl +++ b/definitions/tools/pvacfuse.cwl @@ -22,7 +22,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v4" #TODO: replace with final release version + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v5" #TODO: replace with final release version - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacseq.cwl b/definitions/tools/pvacseq.cwl index 2203c490..cd09b28b 100644 --- a/definitions/tools/pvacseq.cwl +++ b/definitions/tools/pvacseq.cwl @@ -22,7 +22,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v4" #TODO: replace with final release version + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v5" #TODO: replace with final release version - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacvector.cwl b/definitions/tools/pvacvector.cwl index 41712848..82e7899c 100644 --- a/definitions/tools/pvacvector.cwl +++ b/definitions/tools/pvacvector.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v4" + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v5" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) From 0d6bea22413d67204e5231335cdb44607f20403f Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 5 Apr 2023 13:30:34 -0500 Subject: [PATCH 07/10] Add ensembl version to reference fasta --- definitions/tools/pvacbind.cwl | 4 ++-- definitions/tools/pvacfuse.cwl | 4 ++-- definitions/tools/pvacseq.cwl | 4 ++-- definitions/tools/pvacvector.cwl | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/definitions/tools/pvacbind.cwl b/definitions/tools/pvacbind.cwl index fec458f4..23e2c501 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", - "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.pep.all.fa.gz", + "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.101.pep.all.fa.gz", { position: 5, valueFrom: $(runtime.outdir) }, ] requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v5" + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v12" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacfuse.cwl b/definitions/tools/pvacfuse.cwl index d6083917..52ff560c 100644 --- a/definitions/tools/pvacfuse.cwl +++ b/definitions/tools/pvacfuse.cwl @@ -16,13 +16,13 @@ arguments: [ "/usr/local/bin/pvacfuse", "run", "--iedb-install-directory", "/opt/iedb", - "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.pep.all.fa.gz", + "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.101.pep.all.fa.gz", { position: 5, valueFrom: "pvacfuse_predictions" }, ] requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v5" #TODO: replace with final release version + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v12" #TODO: replace with final release version - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacseq.cwl b/definitions/tools/pvacseq.cwl index cd09b28b..d63b96e3 100644 --- a/definitions/tools/pvacseq.cwl +++ b/definitions/tools/pvacseq.cwl @@ -15,14 +15,14 @@ arguments: [ { valueFrom: " && ", shellQuote: false }, "/usr/local/bin/pvacseq", "run", "--iedb-install-directory", "/opt/iedb", - "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.pep.all.fa.gz", + "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.101.pep.all.fa.gz", "--pass-only", { position: 5, valueFrom: "pvacseq_predictions" }, ] requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v5" #TODO: replace with final release version + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v12" #TODO: replace with final release version - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacvector.cwl b/definitions/tools/pvacvector.cwl index 82e7899c..7b869493 100644 --- a/definitions/tools/pvacvector.cwl +++ b/definitions/tools/pvacvector.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v5" + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v12" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) From dd4de17c72ff6bdd7f33d18b4edd810033a5fae7 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Thu, 6 Apr 2023 12:46:17 -0500 Subject: [PATCH 08/10] Make peptide fasta an input --- definitions/pipelines/immuno.cwl | 7 +++++++ definitions/subworkflows/pvacseq.cwl | 3 +++ definitions/tools/pvacfuse.cwl | 5 ++++- definitions/tools/pvacseq.cwl | 5 ++++- 4 files changed, 18 insertions(+), 2 deletions(-) diff --git a/definitions/pipelines/immuno.cwl b/definitions/pipelines/immuno.cwl index b2d80278..e0c14b70 100644 --- a/definitions/pipelines/immuno.cwl +++ b/definitions/pipelines/immuno.cwl @@ -450,6 +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. + peptide_fasta: + type: File? + label: "run_reference_proteome_similarity: sets an option whether to run reference proteome similarity or not" + doc: | + 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" @@ -1282,6 +1287,7 @@ steps: net_chop_threshold: net_chop_threshold netmhc_stab: netmhc_stab run_reference_proteome_similarity: run_reference_proteome_similarity + 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 @@ -1312,6 +1318,7 @@ steps: top_score_metric: top_score_metric net_chop_threshold: net_chop_threshold run_reference_proteome_similarity: run_reference_proteome_similarity + peptide_fasta: peptide_fasta additional_report_columns: additional_report_columns fasta_size: fasta_size downstream_sequence_length: downstream_sequence_length diff --git a/definitions/subworkflows/pvacseq.cwl b/definitions/subworkflows/pvacseq.cwl index 9ba3e257..3040c707 100644 --- a/definitions/subworkflows/pvacseq.cwl +++ b/definitions/subworkflows/pvacseq.cwl @@ -109,6 +109,8 @@ inputs: type: boolean? run_reference_proteome_similarity: type: boolean? + peptide_fasta: + type: File? n_threads: type: int? variants_to_table_fields: @@ -214,6 +216,7 @@ steps: net_chop_threshold: net_chop_threshold netmhc_stab: netmhc_stab run_reference_proteome_similarity: run_reference_proteome_similarity + peptide_fasta: peptide_fasta n_threads: n_threads tumor_purity: tumor_purity aggregate_inclusion_binding_threshold: aggregate_inclusion_binding_threshold diff --git a/definitions/tools/pvacfuse.cwl b/definitions/tools/pvacfuse.cwl index 52ff560c..e495b552 100644 --- a/definitions/tools/pvacfuse.cwl +++ b/definitions/tools/pvacfuse.cwl @@ -16,7 +16,6 @@ arguments: [ "/usr/local/bin/pvacfuse", "run", "--iedb-install-directory", "/opt/iedb", - "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.101.pep.all.fa.gz", { position: 5, valueFrom: "pvacfuse_predictions" }, ] requirements: @@ -113,6 +112,10 @@ inputs: type: boolean? inputBinding: prefix: "--run-reference-proteome-similarity" + peptide_fasta: + type: File? + inputBinding: + prefix: "--peptide-fasta" additional_report_columns: type: - "null" diff --git a/definitions/tools/pvacseq.cwl b/definitions/tools/pvacseq.cwl index d63b96e3..26bd9c9a 100644 --- a/definitions/tools/pvacseq.cwl +++ b/definitions/tools/pvacseq.cwl @@ -15,7 +15,6 @@ arguments: [ { valueFrom: " && ", shellQuote: false }, "/usr/local/bin/pvacseq", "run", "--iedb-install-directory", "/opt/iedb", - "--peptide-fasta", "/opt/reference_fasta/Homo_sapiens.GRCh38.101.pep.all.fa.gz", "--pass-only", { position: 5, valueFrom: "pvacseq_predictions" }, ] @@ -100,6 +99,10 @@ inputs: type: boolean? inputBinding: prefix: "--run-reference-proteome-similarity" + peptide_fasta: + type: File? + inputBinding: + prefix: "--peptide-fasta" top_score_metric: type: - "null" From fbe0441cfb8b4ee86293e24abbfa4588016e1004 Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 31 May 2023 15:39:41 -0500 Subject: [PATCH 09/10] Update to release candidate v19 --- definitions/tools/pvacbind.cwl | 2 +- definitions/tools/pvacfuse.cwl | 2 +- definitions/tools/pvacseq.cwl | 2 +- definitions/tools/pvacvector.cwl | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/definitions/tools/pvacbind.cwl b/definitions/tools/pvacbind.cwl index 23e2c501..c494552d 100644 --- a/definitions/tools/pvacbind.cwl +++ b/definitions/tools/pvacbind.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v12" + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v19" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacfuse.cwl b/definitions/tools/pvacfuse.cwl index e495b552..15a5a4e5 100644 --- a/definitions/tools/pvacfuse.cwl +++ b/definitions/tools/pvacfuse.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v12" #TODO: replace with final release version + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v19" #TODO: replace with final release version - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacseq.cwl b/definitions/tools/pvacseq.cwl index 26bd9c9a..c2efb787 100644 --- a/definitions/tools/pvacseq.cwl +++ b/definitions/tools/pvacseq.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v12" #TODO: replace with final release version + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v19" #TODO: replace with final release version - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacvector.cwl b/definitions/tools/pvacvector.cwl index 7b869493..5309e774 100644 --- a/definitions/tools/pvacvector.cwl +++ b/definitions/tools/pvacvector.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v12" + dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v19" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) From bd72727b42d38bab387d72720d89d704e45d371e Mon Sep 17 00:00:00 2001 From: Susanna Kiwala Date: Wed, 21 Jun 2023 13:25:32 -0500 Subject: [PATCH 10/10] Upgrade to official 4.0.0 release --- definitions/tools/pvacbind.cwl | 2 +- definitions/tools/pvacfuse.cwl | 2 +- definitions/tools/pvacseq.cwl | 2 +- definitions/tools/pvacvector.cwl | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/definitions/tools/pvacbind.cwl b/definitions/tools/pvacbind.cwl index c494552d..8c80279f 100644 --- a/definitions/tools/pvacbind.cwl +++ b/definitions/tools/pvacbind.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v19" + dockerPull: "griffithlab/pvactools:4.0.0" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacfuse.cwl b/definitions/tools/pvacfuse.cwl index 15a5a4e5..631fe693 100644 --- a/definitions/tools/pvacfuse.cwl +++ b/definitions/tools/pvacfuse.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v19" #TODO: replace with final release version + dockerPull: "griffithlab/pvactools:4.0.0" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacseq.cwl b/definitions/tools/pvacseq.cwl index c2efb787..2ad53bae 100644 --- a/definitions/tools/pvacseq.cwl +++ b/definitions/tools/pvacseq.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v19" #TODO: replace with final release version + dockerPull: "griffithlab/pvactools:4.0.0" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads) diff --git a/definitions/tools/pvacvector.cwl b/definitions/tools/pvacvector.cwl index 5309e774..c507ade9 100644 --- a/definitions/tools/pvacvector.cwl +++ b/definitions/tools/pvacvector.cwl @@ -21,7 +21,7 @@ arguments: [ requirements: - class: ShellCommandRequirement - class: DockerRequirement - dockerPull: "susannakiwala/pvactools:4.0.0_rc_pvacview_v19" + dockerPull: "griffithlab/pvactools:4.0.0" - class: ResourceRequirement ramMin: 16000 coresMin: $(inputs.n_threads)