From 2460c9cbc66cc472a84922509846f3ef911ec0f7 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:02:23 +0100 Subject: [PATCH 01/16] rename params.custom_extra_files to params.vep_custom_extra_files and add parameter settings --- nextflow.config | 2 +- nextflow_schema.json | 11 ++++++----- workflows/oncorefiner.nf | 2 +- 3 files changed, 8 insertions(+), 7 deletions(-) diff --git a/nextflow.config b/nextflow.config index a3778e5..d4ba7cd 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,7 +22,7 @@ params { vep_cache_version = 112 vep_plugin_files = null vep_cache = null - custom_extra_files = null + vep_custom_extra_files = null // Vcfanno vcfanno_toml = null diff --git a/nextflow_schema.json b/nextflow_schema.json index 0745a8e..a2566e2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -80,8 +80,7 @@ "type": "string", "default": "homo_sapiens", "enum": ["homo_sapiens"], - "description": "Species of the reference genome. E.g. `--species homo_sapiens`.", - "help_text": "" + "description": "Species of the reference genome. E.g. `--species homo_sapiens`." } } }, @@ -115,6 +114,11 @@ "mimetype": "text/csv", "schema": "assets/vep_plugin_files_schema.json" }, + "vep_custom_extra_files": { + "type": "string", + "description": "Path to extra sample-specific files to be used by VEP for custom annotation (optional).", + "fa_icon": "fas fa-copy" + }, "vcfanno_extra": { "type": "string", "exists": true, @@ -339,9 +343,6 @@ }, "sv_vcf": { "type": "string" - }, - "custom_extra_files": { - "type": "string" } } } diff --git a/workflows/oncorefiner.nf b/workflows/oncorefiner.nf index 64ecec5..6f2bec6 100644 --- a/workflows/oncorefiner.nf +++ b/workflows/oncorefiner.nf @@ -138,7 +138,7 @@ workflow ONCOREFINER { // VEP RESEARCH_FILTERING.out.vcf .map { meta, vcf -> - def custom_extra_files = params.custom_extra_files ? file(params.custom_extra_files) : [] + def custom_extra_files = params.vep_custom_extra_files ? file(params.vep_custom_extra_files) : [] tuple(meta, vcf, custom_extra_files) } .set { ch_vep_snv } From 3fe45426fd91d1aadd66684f6acfeb5993881655 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:27:02 +0100 Subject: [PATCH 02/16] fixed sv and snv vcf parameters --- nextflow_schema.json | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index a2566e2..f8b56b8 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -29,6 +29,23 @@ "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open" }, + "snv_vcf": { + "type": "string", + "fa_icon": "fas fa-file", + "help_text": "Path to somatic SNV/INDEL VCF file.", + "description": "Path to somatic SNV/INDEL VCF file.", + "pattern": "^\\S+\\.vcf(\\.gz)?$", + "format": "file-path", + "exists": true + }, + "sv_vcf": { + "type": "string", + "fa_icon": "fas fa-file", + "description": "Path to somatic SV VCF file.", + "pattern": "^\\S+\\.vcf(\\.gz)?$", + "format": "file-path", + "exists": true + }, "email": { "type": "string", "description": "Email address for completion summary.", @@ -116,7 +133,7 @@ }, "vep_custom_extra_files": { "type": "string", - "description": "Path to extra sample-specific files to be used by VEP for custom annotation (optional).", + "description": "Path to extra sample-specific files to be used by VEP for custom annotation.", "fa_icon": "fas fa-copy" }, "vcfanno_extra": { @@ -336,13 +353,5 @@ { "$ref": "#/$defs/generic_options" } - ], - "properties": { - "snv_vcf": { - "type": "string" - }, - "sv_vcf": { - "type": "string" - } - } + ] } From f434a62ce97fc4f015ae784a2e9e088382b40620 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:28:06 +0100 Subject: [PATCH 03/16] update vep_custom_extra_files --- nextflow_schema.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index f8b56b8..0053717 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -134,7 +134,8 @@ "vep_custom_extra_files": { "type": "string", "description": "Path to extra sample-specific files to be used by VEP for custom annotation.", - "fa_icon": "fas fa-copy" + "fa_icon": "fas fa-copy", + "exist": true }, "vcfanno_extra": { "type": "string", From 1d55b1965f548ac6e45e8abc07919629799af3d2 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:31:06 +0100 Subject: [PATCH 04/16] update snv_vcf --- nextflow_schema.json | 1 - 1 file changed, 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 0053717..e7a70d2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -32,7 +32,6 @@ "snv_vcf": { "type": "string", "fa_icon": "fas fa-file", - "help_text": "Path to somatic SNV/INDEL VCF file.", "description": "Path to somatic SNV/INDEL VCF file.", "pattern": "^\\S+\\.vcf(\\.gz)?$", "format": "file-path", From 9af0d7b587db93cbc662d2f69f194af0f0c7f433 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:32:10 +0100 Subject: [PATCH 05/16] update nextflow_schema --- nextflow_schema.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index e7a70d2..7d7bea5 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -96,7 +96,8 @@ "type": "string", "default": "homo_sapiens", "enum": ["homo_sapiens"], - "description": "Species of the reference genome. E.g. `--species homo_sapiens`." + "description": "Species of the reference genome. E.g. `--species homo_sapiens`.", + "help_text": "" } } }, From 66dd6a5d1370ea1019368c4d80d4ed723f12f4f3 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:34:24 +0100 Subject: [PATCH 06/16] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 76e536e..3488b06 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,6 +45,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt - Updated all modules and removed deprecated `ch_versions` to implement latest nf-core changes that use the `versions` topic channel to collect software versions [#34](https://github.com/Clinical-Genomics/oncorefiner/pull/34) - Fixed settings for `add_pr_checklist_comment` to allow action to run on a PR originated from a fork [#45](https://github.com/Clinical-Genomics/oncorefiner/pull/45) - Added `species` parameter to provide information for annotation which was previously hardcoded [#49](https://github.com/Clinical-Genomics/oncorefiner/pull/49) +- Added settings and moved ungrouped parameters to relevant groups [#50](https://github.com/Clinical-Genomics/oncorefiner/pull/50) ### `Dependencies` From 67299962bca1131407bdd70096f994a9a6c0dc91 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:34:45 +0100 Subject: [PATCH 07/16] pre-commit --- docs/parameters.md | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index f6a5812..3305c56 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -10,6 +10,8 @@ Define where the pipeline should find input data and save output data. |-----------|-----------|-----------|-----------|-----------|-----------| | `input` | Path to comma-separated file containing information about the samples in the experiment.
HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.
| `string` | | True | | | `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | | True | | +| `snv_vcf` | Path to somatic SNV/INDEL VCF file. | `string` | | | | +| `sv_vcf` | Path to somatic SV VCF file. | `string` | | | | | `email` | Email address for completion summary.
HelpSet this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.
| `string` | | | | | `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` | | | | @@ -19,9 +21,9 @@ Reference genome related files and options required for the workflow. | Parameter | Description | Type | Default | Required | Hidden | |-----------|-----------|-----------|-----------|-----------|-----------| +| `genome` | Name of the genome reference. (accepted: `GRCh38`\|`GRCh37`)
HelpUse this parameter to specify the ID for the reference genome used. This is then used to annotate the SV and SNV files e.g. `--genome GRCh38`.
| `string` | GRCh38 | | | | `fasta` | Path to FASTA genome file.
HelpIf you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.
| `string` | | | | | `fai` | Path to FASTA genome index file.
HelpIf none provided, will be generated automatically from the FASTA reference
| `string` | | | | -| `genome` | Name of the genome reference. (accepted: `GRCh38`\|`GRCh37`)
HelpUse this parameter to specify the ID for the reference genome used. This is then used to annotate the SV and SNV files e.g. `--genome GRCh38`.
| `string` | GRCh38 | | | | `species` | Species of the reference genome. E.g. `--species homo_sapiens`. (accepted: `homo_sapiens`) | `string` | homo_sapiens | | | ## Annotation options @@ -33,6 +35,7 @@ Annotation related files and options required for the workflow. | `vep_cache_version` | Specify the version of the VEP cache provided to the `--vep_cache` option. | `integer` | 112 | | | | `vep_cache` | Path to vep's cache directory.
HelpIf no directory path is passed, vcf files will not be annotated by vep.
| `string` | | | | | `vep_plugin_files` | Databases used by both named and custom plugins to annotate variants.
HelpPath to a file containing the absolute paths to databases and their indices used by VEP's custom and named plugins resources defined within the vcfanno toml file. One line per resource.
| `string` | | | | +| `vep_custom_extra_files` | Path to extra sample-specific files to be used by VEP for custom annotation. | `string` | | | | | `vcfanno_extra` | Path to a VCF file containing annotations.
HelpCan be used to supply case-specific annotations in addition to those provided using --vcfanno_resources
| `string` | | | | | `vcfanno_resources` | Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.
HelpIf no file is passed, default configurations will be used according to genome build within the context of the pipeline.
| `string` | | | | | `vcfanno_toml` | Path to the vcfanno toml file.
HelpIf no toml is passed, default configurations will be used according to genome build within the context of the pipeline.
| `string` | | | | @@ -74,11 +77,3 @@ Less common options for the pipeline, typically set in a config file. | `help` | Display the help message. | `['boolean', 'string']` | | | | | `help_full` | Display the full detailed help message. | `boolean` | | | | | `show_hidden` | Display hidden parameters in the help message (only works when --help or --help_full are provided). | `boolean` | | | | - -## Other parameters - -| Parameter | Description | Type | Default | Required | Hidden | -|-----------|-----------|-----------|-----------|-----------|-----------| -| `snv_vcf` | | `string` | | | | -| `sv_vcf` | | `string` | | | | -| `custom_extra_files` | | `string` | | | | From b305c31ad7432eb97386788506d62ea5d568340c Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:38:02 +0100 Subject: [PATCH 08/16] pre-commit --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3488b06..3cdcb51 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,7 +45,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt - Updated all modules and removed deprecated `ch_versions` to implement latest nf-core changes that use the `versions` topic channel to collect software versions [#34](https://github.com/Clinical-Genomics/oncorefiner/pull/34) - Fixed settings for `add_pr_checklist_comment` to allow action to run on a PR originated from a fork [#45](https://github.com/Clinical-Genomics/oncorefiner/pull/45) - Added `species` parameter to provide information for annotation which was previously hardcoded [#49](https://github.com/Clinical-Genomics/oncorefiner/pull/49) -- Added settings and moved ungrouped parameters to relevant groups [#50](https://github.com/Clinical-Genomics/oncorefiner/pull/50) +- Added settings and moved ungrouped parameters to relevant groups [#50](https://github.com/Clinical-Genomics/oncorefiner/pull/50) ### `Dependencies` From 3266c54bac932341a7204ec6872686d4ed6f04cb Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:49:22 +0100 Subject: [PATCH 09/16] update params.custom_extra_files to new name --- workflows/oncorefiner.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/workflows/oncorefiner.nf b/workflows/oncorefiner.nf index 6f2bec6..dc14b43 100644 --- a/workflows/oncorefiner.nf +++ b/workflows/oncorefiner.nf @@ -202,7 +202,7 @@ workflow ONCOREFINER { // VEP RESEARCH_FILTERING_SV.out.vcf .map { meta, vcf -> - def custom_extra_files = params.custom_extra_files ? file(params.custom_extra_files) : [] + def custom_extra_files = params.vep_custom_extra_files ? file(params.vep_custom_extra_files) : [] tuple(meta, vcf, custom_extra_files) } .set { ch_vep_sv } From e269bef8126782c384a6945b429f73b5591f6fec Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 14:57:13 +0100 Subject: [PATCH 10/16] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3cdcb51..e5071d0 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,7 +45,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt - Updated all modules and removed deprecated `ch_versions` to implement latest nf-core changes that use the `versions` topic channel to collect software versions [#34](https://github.com/Clinical-Genomics/oncorefiner/pull/34) - Fixed settings for `add_pr_checklist_comment` to allow action to run on a PR originated from a fork [#45](https://github.com/Clinical-Genomics/oncorefiner/pull/45) - Added `species` parameter to provide information for annotation which was previously hardcoded [#49](https://github.com/Clinical-Genomics/oncorefiner/pull/49) -- Added settings and moved ungrouped parameters to relevant groups [#50](https://github.com/Clinical-Genomics/oncorefiner/pull/50) +- Refactored, added settings and moved ungrouped parameters to relevant groups [#50](https://github.com/Clinical-Genomics/oncorefiner/pull/50) ### `Dependencies` From 97394b262403168dec15110c3cf191d8b31c1b29 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 11:12:21 +0100 Subject: [PATCH 11/16] restore files that refer to custom_extra_files parameter --- nextflow.config | 2 +- workflows/oncorefiner.nf | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nextflow.config b/nextflow.config index d4ba7cd..a3778e5 100644 --- a/nextflow.config +++ b/nextflow.config @@ -22,7 +22,7 @@ params { vep_cache_version = 112 vep_plugin_files = null vep_cache = null - vep_custom_extra_files = null + custom_extra_files = null // Vcfanno vcfanno_toml = null diff --git a/workflows/oncorefiner.nf b/workflows/oncorefiner.nf index dc14b43..64ecec5 100644 --- a/workflows/oncorefiner.nf +++ b/workflows/oncorefiner.nf @@ -138,7 +138,7 @@ workflow ONCOREFINER { // VEP RESEARCH_FILTERING.out.vcf .map { meta, vcf -> - def custom_extra_files = params.vep_custom_extra_files ? file(params.vep_custom_extra_files) : [] + def custom_extra_files = params.custom_extra_files ? file(params.custom_extra_files) : [] tuple(meta, vcf, custom_extra_files) } .set { ch_vep_snv } @@ -202,7 +202,7 @@ workflow ONCOREFINER { // VEP RESEARCH_FILTERING_SV.out.vcf .map { meta, vcf -> - def custom_extra_files = params.vep_custom_extra_files ? file(params.vep_custom_extra_files) : [] + def custom_extra_files = params.custom_extra_files ? file(params.custom_extra_files) : [] tuple(meta, vcf, custom_extra_files) } .set { ch_vep_sv } From 8211e3332ab9bfe642e78d3e9c5fba91efcad220 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 11:19:17 +0100 Subject: [PATCH 12/16] Restore schema for params.custom_extra_files and update paramaters documentation. --- docs/parameters.md | 7 ++++++- nextflow_schema.json | 13 ++++++------- 2 files changed, 12 insertions(+), 8 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index 3305c56..ed64e08 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -35,7 +35,6 @@ Annotation related files and options required for the workflow. | `vep_cache_version` | Specify the version of the VEP cache provided to the `--vep_cache` option. | `integer` | 112 | | | | `vep_cache` | Path to vep's cache directory.
HelpIf no directory path is passed, vcf files will not be annotated by vep.
| `string` | | | | | `vep_plugin_files` | Databases used by both named and custom plugins to annotate variants.
HelpPath to a file containing the absolute paths to databases and their indices used by VEP's custom and named plugins resources defined within the vcfanno toml file. One line per resource.
| `string` | | | | -| `vep_custom_extra_files` | Path to extra sample-specific files to be used by VEP for custom annotation. | `string` | | | | | `vcfanno_extra` | Path to a VCF file containing annotations.
HelpCan be used to supply case-specific annotations in addition to those provided using --vcfanno_resources
| `string` | | | | | `vcfanno_resources` | Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource.
HelpIf no file is passed, default configurations will be used according to genome build within the context of the pipeline.
| `string` | | | | | `vcfanno_toml` | Path to the vcfanno toml file.
HelpIf no toml is passed, default configurations will be used according to genome build within the context of the pipeline.
| `string` | | | | @@ -77,3 +76,9 @@ Less common options for the pipeline, typically set in a config file. | `help` | Display the help message. | `['boolean', 'string']` | | | | | `help_full` | Display the full detailed help message. | `boolean` | | | | | `show_hidden` | Display hidden parameters in the help message (only works when --help or --help_full are provided). | `boolean` | | | | + +## Other parameters + +| Parameter | Description | Type | Default | Required | Hidden | +|-----------|-----------|-----------|-----------|-----------|-----------| +| `custom_extra_files` | | `string` | | | | diff --git a/nextflow_schema.json b/nextflow_schema.json index 7d7bea5..6ce1fe7 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -131,12 +131,6 @@ "mimetype": "text/csv", "schema": "assets/vep_plugin_files_schema.json" }, - "vep_custom_extra_files": { - "type": "string", - "description": "Path to extra sample-specific files to be used by VEP for custom annotation.", - "fa_icon": "fas fa-copy", - "exist": true - }, "vcfanno_extra": { "type": "string", "exists": true, @@ -354,5 +348,10 @@ { "$ref": "#/$defs/generic_options" } - ] + ], + "properties": { + "custom_extra_files": { + "type": "string" + } + } } From ab8def1d64650308245db26d93d196817c1cd828 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 11:22:19 +0100 Subject: [PATCH 13/16] Update parameter description for snv_vcf and sv_vcf. --- docs/parameters.md | 4 ++-- nextflow_schema.json | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index ed64e08..3a595e8 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -10,8 +10,8 @@ Define where the pipeline should find input data and save output data. |-----------|-----------|-----------|-----------|-----------|-----------| | `input` | Path to comma-separated file containing information about the samples in the experiment.
HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.
| `string` | | True | | | `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | | True | | -| `snv_vcf` | Path to somatic SNV/INDEL VCF file. | `string` | | | | -| `sv_vcf` | Path to somatic SV VCF file. | `string` | | | | +| `snv_vcf` | Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor–normal analyses. | `string` | | | | +| `sv_vcf` | Path to a VCF file containing somatic structural variants (SVs) to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor–normal analyses. | `string` | | | | | `email` | Email address for completion summary.
HelpSet this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.
| `string` | | | | | `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` | | | | diff --git a/nextflow_schema.json b/nextflow_schema.json index 6ce1fe7..841e6bc 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -32,7 +32,7 @@ "snv_vcf": { "type": "string", "fa_icon": "fas fa-file", - "description": "Path to somatic SNV/INDEL VCF file.", + "description": "Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor–normal analyses.", "pattern": "^\\S+\\.vcf(\\.gz)?$", "format": "file-path", "exists": true @@ -40,7 +40,7 @@ "sv_vcf": { "type": "string", "fa_icon": "fas fa-file", - "description": "Path to somatic SV VCF file.", + "description": "Path to a VCF file containing somatic structural variants (SVs) to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor–normal analyses.", "pattern": "^\\S+\\.vcf(\\.gz)?$", "format": "file-path", "exists": true From 6d1b708eb911dbd421808adea4dca687b5f3b81c Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 11:42:22 +0100 Subject: [PATCH 14/16] update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4f8e880..843b5eb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -45,7 +45,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt - Updated all modules and removed deprecated `ch_versions` to implement latest nf-core changes that use the `versions` topic channel to collect software versions [#34](https://github.com/Clinical-Genomics/oncorefiner/pull/34) - Fixed settings for `add_pr_checklist_comment` to allow action to run on a PR originated from a fork [#45](https://github.com/Clinical-Genomics/oncorefiner/pull/45) - Added `species` parameter to provide information for annotation which was previously hardcoded [#49](https://github.com/Clinical-Genomics/oncorefiner/pull/49) -- Refactored, added settings and moved ungrouped parameters to relevant groups [#50](https://github.com/Clinical-Genomics/oncorefiner/pull/50) +- Added settings and moved ungrouped parameters to relevant groups [#50](https://github.com/Clinical-Genomics/oncorefiner/pull/50) ### `Dependencies` From d2572dbd5547f40f25fcf63c4f588dd8d8cb2751 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Tue, 17 Mar 2026 11:46:26 +0100 Subject: [PATCH 15/16] Update nextflow_schema.json Co-authored-by: Eva C <29628428+fevac@users.noreply.github.com> --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index c06fe0a..25ab6f2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -33,7 +33,7 @@ "type": "string", "fa_icon": "fas fa-file", "description": "Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor\u2013normal analyses.", - "pattern": "^\\S+\\.vcf(\\.gz)?$", + "pattern": "^\\S+\\.vcf\\.gz$", "format": "file-path", "exists": true }, From 40fb3444d5d163dd13959936bfac11d826cf8389 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 11:48:01 +0100 Subject: [PATCH 16/16] Update nextflow_schema. --- docs/parameters.md | 4 ++-- nextflow_schema.json | 6 +++--- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index 6dd852c..a626bf4 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -10,8 +10,8 @@ Define where the pipeline should find input data and save output data. |-----------|-----------|-----------|-----------|-----------|-----------| | `input` | Path to comma-separated file containing information about the samples in the experiment.
HelpYou will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row.
| `string` | | True | | | `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | | True | | -| `snv_vcf` | Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor–normal analyses. | `string` | | | | -| `sv_vcf` | Path to a VCF file containing somatic structural variants (SVs) to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor–normal analyses. | `string` | | | | +| `snv_vcf` | Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses. | `string` | | | | +| `sv_vcf` | Path to a VCF file containing somatic structural variants (SVs) to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses. | `string` | | | | | `email` | Email address for completion summary.
HelpSet this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.
| `string` | | | | | `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` | | | | diff --git a/nextflow_schema.json b/nextflow_schema.json index 25ab6f2..f0c2862 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -32,7 +32,7 @@ "snv_vcf": { "type": "string", "fa_icon": "fas fa-file", - "description": "Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor\u2013normal analyses.", + "description": "Path to a VCF file containing somatic SNV/INDEL variants to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses.", "pattern": "^\\S+\\.vcf\\.gz$", "format": "file-path", "exists": true @@ -40,8 +40,8 @@ "sv_vcf": { "type": "string", "fa_icon": "fas fa-file", - "description": "Path to a VCF file containing somatic structural variants (SVs) to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor\u2013normal analyses.", - "pattern": "^\\S+\\.vcf(\\.gz)?$", + "description": "Path to a VCF file containing somatic structural variants (SVs) to be processed by the pipeline. The VCF may include one or multiple samples. Typically, this is a single tumor sample for tumor-only analyses, or both tumor and matched normal samples for tumor-normal analyses.", + "pattern": "^\\S+\\.vcf\\.gz$", "format": "file-path", "exists": true },