From d30a2dab7b3987dbf9427fff9e6c9fed07ca011f Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 12 Mar 2026 14:39:04 +0100 Subject: [PATCH 01/34] update project description in .nf-core.yml --- .nf-core.yml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 07f5253..e19b1e9 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -19,10 +19,9 @@ nf_core_version: 3.5.2 repository_type: pipeline template: author: Clinical Genomics Stockholm - description: Customizable post-processing and extension layer built on top of Oncoanalyser - that adapts its outputs to clinical and operational needs, adds missing analyses, - and ensures flexibility for evolving standards while retaining Oncoanalyser robust - core + description: Customizable post-processing and extension layer for Oncoanalyser that adapts + its outputs according to clinical and operational needs, adds missing analyses, and + ensures flexibility for evolving standards while retaining Oncoanalyser's robust core. force: false is_nfcore: false name: oncorefiner From da7f3d9c556441a0c350705da38a0b68205ca3ab Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 12 Mar 2026 14:48:40 +0100 Subject: [PATCH 02/34] update parameters.md --- docs/parameters.md | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/docs/parameters.md b/docs/parameters.md index 0a3881d..c122a39 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -1,4 +1,4 @@ -# nf-core/oncorefiner pipeline parameters +# Clinical-Genomics/oncorefiner pipeline parameters Customizable post-processing and extension layer built on top of Oncoanalyser that adapts its outputs to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser robust core @@ -8,7 +8,7 @@ Define where the pipeline should find input data and save output data. | Parameter | Description | Type | Default | Required | Hidden | |-----------|-----------|-----------|-----------|-----------|-----------| -| `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. See [usage docs](https://nf-co.re/oncorefiner/usage#samplesheet-input).
| `string` | | True | | +| `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 | | | `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` | | | | @@ -19,11 +19,9 @@ Reference genome related files and options required for the workflow. | Parameter | Description | Type | Default | Required | Hidden | |-----------|-----------|-----------|-----------|-----------|-----------| -| `genome` | Name of iGenomes reference.
HelpIf using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`.

See the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.
| `string` | | | | -| `fasta` | Path to FASTA genome file.
HelpThis parameter is *mandatory* if `--genome` is not specified. If 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` | | | | +| `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` | | | | -| `igenomes_ignore` | Do not load the iGenomes reference config.
HelpDo not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.
| `boolean` | | | True | -| `igenomes_base` | The base path to the igenomes reference files | `string` | s3://ngi-igenomes/igenomes/ | | True | ## Annotation options @@ -75,3 +73,11 @@ 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 9149209753b17af65f5d427aec1d8dc2383eaf9c Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 12 Mar 2026 14:48:49 +0100 Subject: [PATCH 03/34] pre-commit --- .nf-core.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index e19b1e9..a014dc2 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -20,7 +20,7 @@ repository_type: pipeline template: author: Clinical Genomics Stockholm description: Customizable post-processing and extension layer for Oncoanalyser that adapts - its outputs according to clinical and operational needs, adds missing analyses, and + its outputs according to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser's robust core. force: false is_nfcore: false From 6ea04522dbcfa842089c5f6c09268919dcc63c62 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 12 Mar 2026 14:52:59 +0100 Subject: [PATCH 04/34] update changelog --- CHANGELOG.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ed6ff80..73d93f8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,7 +20,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt - Added pre-commit hook for automatic generation of parameters documentation [#25](https://github.com/Clinical-Genomics/oncorefiner/pull/25) - Added Nextflow strict syntax compatibility [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) -### Changed +### `Changed` - Updated PR template, PR checklist, feature request template, bug report template and issue template chooser [#24](https://github.com/Clinical-Genomics/oncorefiner/pull/24) - Updated nf-schema to 2.6.1 [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) @@ -30,10 +30,10 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt ### `Fixed` - Removed snv_vcf_tbi and sv_vcf_tbi parameter. VCF indexes are now automatically detected [#9](https://github.com/Clinical-Genomics/oncorefiner/pull/9) -- Renamed pipeline from postprocessing to oncorefiner []() +- Renamed pipeline from postprocessing to oncorefiner [#10](https://github.com/Clinical-Genomics/oncorefiner/pull/10) - Fixed linting issues [#20](https://github.com/Clinical-Genomics/oncorefiner/pull/20) - Fixed nf-test to run a functional default test, and generated a snapshot [#26](https://github.com/Clinical-Genomics/oncorefiner/pull/26) -- Added missing description to bug_report.yml [32](https://github.com/Clinical-Genomics/oncorefiner/pull/32) +- Added missing description in bug report template [32](https://github.com/Clinical-Genomics/oncorefiner/pull/32) - Updated template settings to set organisation to `Clinical-Genomics` and skip unused features `igenomes` and `fastqc` [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) - Refactored `genome` parameter to have default value 'GRCh38' and no longer refer to igenomes [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) - Updated linting config to fix linting issues and re-added/removed checks for files where nf-core file structure is no longer required [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) From bad6f1cb5cdaaf0b7b47d53e9eccdb713638fbef Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 12 Mar 2026 14:56:39 +0100 Subject: [PATCH 05/34] update changelog --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 73d93f8..4cd05dc 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -37,10 +37,10 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt - Updated template settings to set organisation to `Clinical-Genomics` and skip unused features `igenomes` and `fastqc` [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) - Refactored `genome` parameter to have default value 'GRCh38' and no longer refer to igenomes [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) - Updated linting config to fix linting issues and re-added/removed checks for files where nf-core file structure is no longer required [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) -- Updated template for nf-core/tools version 3.5.2 to apply updated settings and changes missed in previous template update ([14](https://github.com/Clinical-Genomics/oncorefiner/pull/14)) [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) +- Updated template for nf-core/tools version 3.5.2 to apply updated settings and changes missed in previous template update ([#14](https://github.com/Clinical-Genomics/oncorefiner/pull/14)) [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) - Fixed prepare_references config that was defined but not used [36](https://github.com/Clinical-Genomics/oncorefiner/pull/36) - Fixed bug and formatting in feature request template [#39](https://github.com/Clinical-Genomics/oncorefiner/pull/39) -- Fixed merge mistake introduced in [#25](https://github.com/Clinical-Genomics/oncorefiner/pull/25) [#41](https://github.com/Clinical-Genomics/oncorefiner/pull/41) +- Fixed merge mistake in `.nf-core.yml` introduced in previous PR ([#25](https://github.com/Clinical-Genomics/oncorefiner/pull/25)) [#41](https://github.com/Clinical-Genomics/oncorefiner/pull/41) - Added necessary GITHUB_TOKEN permissions for action add_pr_checklist_comment [#42](https://github.com/Clinical-Genomics/oncorefiner/pull/42) - 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) From f3fcb3cd1dde511be9f7cb1af11f1bdc5999856e Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 13 Mar 2026 11:09:45 +0100 Subject: [PATCH 06/34] add template update instructions to contributing.md --- .github/CONTRIBUTING.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 2cf6f3c..bf2679c 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -102,6 +102,14 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). +## Update template + +Since this is not an nf-core pipeline, the template is not automatically updated with the nf-core tools. Follow these step to update the template: + +1. Update the `TEMPLATE` branch by running `nf-core pipelines sync`. Fix any merge conflicts and open a PR to then merge the changes. +1. Open a PR to merge the `TEMPLATE` branch into `dev` to update the template files in the main codebase. + + ## GitHub Codespaces This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. From d2a98bd0cf7c825b0eabba51901393eb6ebb1050 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 13 Mar 2026 11:10:53 +0100 Subject: [PATCH 07/34] add template update instructions to contributing.md --- .github/CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index bf2679c..615f1a0 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -104,7 +104,7 @@ For overview images and other documents we follow the nf-core [style guidelines ## Update template -Since this is not an nf-core pipeline, the template is not automatically updated with the nf-core tools. Follow these step to update the template: +Since this is not an nf-core pipeline, the nf-core tools template is not automatically updated in the `TEMPLATE` branch. Follow these step to update the template: 1. Update the `TEMPLATE` branch by running `nf-core pipelines sync`. Fix any merge conflicts and open a PR to then merge the changes. 1. Open a PR to merge the `TEMPLATE` branch into `dev` to update the template files in the main codebase. From 617bf49918476d1f74a2249703937a5940c548b7 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 13 Mar 2026 16:12:19 +0100 Subject: [PATCH 08/34] Add installation instructions to contributing --- .github/CONTRIBUTING.md | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 615f1a0..33899f9 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -21,6 +21,13 @@ If you'd like to write some code for Clinical-Genomics/oncorefiner, the standard If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). +## Installation and dependencies for development + +In order to run the pipeline, develop and test your changes locally, we recommend that you set up: + +- A conda environment with `nextflow` and `nf-core` tools. - For this, follow the instructions from the [nf-core documentation](https://nf-co.re/docs/nf-core-tools/installation). Additional information about [Installation of nf-core dependencies](https://nf-co.re/docs/usage/getting_started/installation/) is also available, if needed. +- Install Docker (https://docs.docker.com/engine/install/) and make sure the daemon is running when you want to run the tests locally. + ## Tests You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: From acb8b3c7b577adaa73fe55c592b467956646ab21 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 13 Mar 2026 16:54:56 +0100 Subject: [PATCH 09/34] update installation instructions to contributing --- .github/CONTRIBUTING.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 33899f9..288ab79 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -28,6 +28,8 @@ In order to run the pipeline, develop and test your changes locally, we recommen - A conda environment with `nextflow` and `nf-core` tools. - For this, follow the instructions from the [nf-core documentation](https://nf-co.re/docs/nf-core-tools/installation). Additional information about [Installation of nf-core dependencies](https://nf-co.re/docs/usage/getting_started/installation/) is also available, if needed. - Install Docker (https://docs.docker.com/engine/install/) and make sure the daemon is running when you want to run the tests locally. +Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. + ## Tests You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command: From 5465fa5fdfb5d5de131a71cb10e07292f96a065d Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 13 Mar 2026 16:58:12 +0100 Subject: [PATCH 10/34] update contributors --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8245dd3..1b0d862 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ For more details about the output files and reports, please refer to the [output Clinical-Genomics/oncorefiner was originally written by Clinical Genomics Stockholm. -We thank the following people for their extensive assistance in the development of this pipeline: [Eva Caceres](https://github.com/fevac), [Kristine Bilgrav Sæther](https://github.com/kristinebilgrav) +We thank the following people for their extensive assistance in the development of this pipeline: [Eva Caceres](https://github.com/fevac), [Kristine Bilgrav Sæther](https://github.com/kristinebilgrav), [Beatriz Sá Vinhas](https://github.com/beatrizsavinhas) and [Mathias Johansson](https://github.com/mathiasbio). ## Contributions and Support From 53a82b3955d50b3239e6ee0140b3e353372afd3b Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 13 Mar 2026 17:02:10 +0100 Subject: [PATCH 11/34] re-arrange contributing.md --- .github/CONTRIBUTING.md | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 288ab79..3a58688 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -107,17 +107,16 @@ Please use the following naming schemes, to make it easy to understand what is g If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core pipelines bump-version --nextflow . [min-nf-version]` -### Images and figures - -For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). - -## Update template +### Update nf-core template -Since this is not an nf-core pipeline, the nf-core tools template is not automatically updated in the `TEMPLATE` branch. Follow these step to update the template: +Since this is not an nf-core pipeline, the nf-core template is not automatically updated in the `TEMPLATE` branch. Follow these step to update the template: 1. Update the `TEMPLATE` branch by running `nf-core pipelines sync`. Fix any merge conflicts and open a PR to then merge the changes. 1. Open a PR to merge the `TEMPLATE` branch into `dev` to update the template files in the main codebase. +### Images and figures + +For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). ## GitHub Codespaces From 7a2c86567b4faed1998777c5c98e7508e7403060 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 13 Mar 2026 17:19:00 +0100 Subject: [PATCH 12/34] add information on PR and reviews in contributing --- .github/CONTRIBUTING.md | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 3a58688..f07af42 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -21,6 +21,37 @@ If you'd like to write some code for Clinical-Genomics/oncorefiner, the standard If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). +### Pull Requests + +When opening a pull request to suggest changes to the code, please make sure to follow the [Pipeline contribution conventions](#pipeline-contribution-conventions) for the code and to fill in the necessary information in the pull request template as well as address all points in the `PR checklist`. + +#### PR title conventions + +We have implemented a standardised PR title format to make it easier to understand the type of change being proposed at a glance. +Addionally, there is an automated check for every PR that will only allow mergere if the title follow one of the following formats: + + - feat: A new feature + - fix: A bug fix + - docs: Documentation only changes + - style: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc) + - refactor: A code change that neither fixes a bug nor adds a feature + - perf: A code change that improves performance + - test: Adding missing tests or correcting existing tests + - build: Changes that affect the build system or external dependencies (example scopes: gulp, broccoli, npm) + - ci: Changes to our CI configuration files and scripts (example scopes: Travis, Circle, BrowserStack, SauceLabs) + - chore: Other changes that don't modify src or test files + - revert: Reverts a previous commit + +#### Review + +When reviewing a PR, make sure to check that: + +- The code follows the [Pipeline contribution conventions](#pipeline-contribution-conventions). +- The information in the PR (and related issue) is clear and sufficient to understand the change and the motivation for it - title, description and entry in `CHANGELOG.md`, if applicable. +- All the items in the `PR checklist` have been addressed, the changes are well documented and the tests are passing. + +Be positive and constructive in your review, and whenever possible offer suggestions for improvement rather than just pointing out issues. + ## Installation and dependencies for development In order to run the pipeline, develop and test your changes locally, we recommend that you set up: From f2edb4e387b38b1ef41b3647d1f1785ead2c3077 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 13 Mar 2026 17:23:39 +0100 Subject: [PATCH 13/34] fix linting issues --- .nf-core.yml | 1 + ro-crate-metadata.json | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.nf-core.yml b/.nf-core.yml index a014dc2..c88c876 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -14,6 +14,7 @@ lint: - .prettierignore - assets/sendmail_template.txt - docs/README.md + - .github/CONTRIBUTING.md multiqc_config: false nf_core_version: 3.5.2 repository_type: pipeline diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index ed73984..8acbd11 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -23,7 +23,7 @@ "@type": "Dataset", "creativeWorkStatus": "InProgress", "datePublished": "2026-03-05T15:49:14+00:00", - "description": "# Clinical-Genomics/oncorefiner\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/Clinical-Genomics/oncorefiner)\n[![GitHub Actions CI Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/Clinical-Genomics/oncorefiner)\n\n## Introduction\n\n**Clinical-Genomics/oncorefiner** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run Clinical-Genomics/oncorefiner \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the [output documentation](.github/docs/output.md).\n\n## Credits\n\nClinical-Genomics/oncorefiner was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline: [Eva Caceres](https://github.com/fevac), [Kristine Bilgrav S\u00e6ther](https://github.com/kristinebilgrav)\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "description": "# Clinical-Genomics/oncorefiner\n\n[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/Clinical-Genomics/oncorefiner)\n[![GitHub Actions CI Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml)\n[![GitHub Actions Linting Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.10.0-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)\n[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.5.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.5.2)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/Clinical-Genomics/oncorefiner)\n\n## Introduction\n\n**Clinical-Genomics/oncorefiner** is a bioinformatics pipeline that ...\n\n\n\n\n2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run Clinical-Genomics/oncorefiner \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the [output documentation](.github/docs/output.md).\n\n## Credits\n\nClinical-Genomics/oncorefiner was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline: [Eva Caceres](https://github.com/fevac), [Kristine Bilgrav S\u00e6ther](https://github.com/kristinebilgrav), [Beatriz S\u00e1 Vinhas](https://github.com/beatrizsavinhas) and [Mathias Johansson](https://github.com/mathiasbio).\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", "hasPart": [ { "@id": "main.nf" From fb07914016a100a78ef1354ef9a3601002e281e8 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 13 Mar 2026 17:26:31 +0100 Subject: [PATCH 14/34] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4cd05dc..30d4082 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -26,6 +26,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt - Updated nf-schema to 2.6.1 [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) - Updated minimum Nextflow version to 25.10.0 [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) - Added wgs-cancer-pipeline projects list in the issue templates [#37](https://github.com/Clinical-Genomics/oncorefiner/pull/37) +- Updated documentation [#48](https://github.com/Clinical-Genomics/oncorefiner/pull/48) ### `Fixed` From 4a374da904ebc47f9d712dbcced52ee9292ee87a Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 09:23:21 +0100 Subject: [PATCH 15/34] update CONTRIBUTING.md --- .github/CONTRIBUTING.md | 26 +++++++++++++------------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index f07af42..0a2b801 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -28,19 +28,19 @@ When opening a pull request to suggest changes to the code, please make sure to #### PR title conventions We have implemented a standardised PR title format to make it easier to understand the type of change being proposed at a glance. -Addionally, there is an automated check for every PR that will only allow mergere if the title follow one of the following formats: - - - feat: A new feature - - fix: A bug fix - - docs: Documentation only changes - - style: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc) - - refactor: A code change that neither fixes a bug nor adds a feature - - perf: A code change that improves performance - - test: Adding missing tests or correcting existing tests - - build: Changes that affect the build system or external dependencies (example scopes: gulp, broccoli, npm) - - ci: Changes to our CI configuration files and scripts (example scopes: Travis, Circle, BrowserStack, SauceLabs) - - chore: Other changes that don't modify src or test files - - revert: Reverts a previous commit +Addionally, there is an automated check for every PR that will only allow mergere if the title adheres to one of the following formats: + +- feat: A new feature +- fix: A bug fix +- docs: Documentation only changes +- style: Changes that do not affect the meaning of the code (white-space, formatting, missing semi-colons, etc) +- refactor: A code change that neither fixes a bug nor adds a feature +- perf: A code change that improves performance +- test: Adding missing tests or correcting existing tests +- build: Changes that affect the build system or external dependencies (example scopes: gulp, broccoli, npm) +- ci: Changes to our CI configuration files and scripts (example scopes: Travis, Circle, BrowserStack, SauceLabs) +- chore: Other changes that don't modify src or test files +- revert: Reverts a previous commit #### Review From 77527492a3011028b133af2b2f81794093d6ecb3 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 10:43:01 +0100 Subject: [PATCH 16/34] refactor changelog --- CHANGELOG.md | 62 ++++++++++++++++++++++++++-------------------------- 1 file changed, 31 insertions(+), 31 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 30d4082..d3b223a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -9,42 +9,42 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt ### `Added` -- Added Ensembl VEP annotation for SNV vcf file [#1](https://github.com/Clinical-Genomics/oncorefiner/pull/1) -- Added VCFANNO annotation for SNV vcf file [#2](https://github.com/Clinical-Genomics/oncorefiner/pull/2) -- Added filtering for SNV vcf file [#3](https://github.com/Clinical-Genomics/oncorefiner/pull/3) -- Added annotation for SV vcf file [#4](https://github.com/Clinical-Genomics/oncorefiner/pull/4) -- Added filtering for SV vcf file [#5](https://github.com/Clinical-Genomics/oncorefiner/pull/5) -- Added small test profile. The related test dataset have been added as a branch called oncorefiner under [Clinical-Genomics/test-datasets](https://github.com/Clinical-Genomics/test-datasets/tree/oncorefiner) [#8](https://github.com/Clinical-Genomics/oncorefiner/pull/8) -- Added CI checks for `Conventional PR title`, `Updated changelog` and `Add PR checklist comment` [#18](https://github.com/Clinical-Genomics/oncorefiner/pull/18) -- Added parameters documentation [#25](https://github.com/Clinical-Genomics/oncorefiner/pull/25) -- Added pre-commit hook for automatic generation of parameters documentation [#25](https://github.com/Clinical-Genomics/oncorefiner/pull/25) -- Added Nextflow strict syntax compatibility [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) +- [#1](https://github.com/Clinical-Genomics/oncorefiner/pull/1) Added Ensembl VEP annotation for SNV vcf file. +- [#2](https://github.com/Clinical-Genomics/oncorefiner/pull/2) Added VCFANNO annotation for SNV vcf file. +- [#3](https://github.com/Clinical-Genomics/oncorefiner/pull/3) Added filtering for SNV vcf file. +- [#4](https://github.com/Clinical-Genomics/oncorefiner/pull/4) Added annotation for SV vcf file. +- [#5](https://github.com/Clinical-Genomics/oncorefiner/pull/5) Added filtering for SV vcf file. +- [#8](https://github.com/Clinical-Genomics/oncorefiner/pull/8) Added small test profile. The related test dataset have been added as a branch called oncorefiner under [Clinical-Genomics/test-datasets](https://github.com/Clinical-Genomics/test-datasets/tree/oncorefiner). +- [#18](https://github.com/Clinical-Genomics/oncorefiner/pull/18) Added CI checks for `Conventional PR title`, `Updated changelog` and `Add PR checklist comment`. +- [#25](https://github.com/Clinical-Genomics/oncorefiner/pull/25) Added parameters documentation. +- [#25](https://github.com/Clinical-Genomics/oncorefiner/pull/25) Added pre-commit hook for automatic generation of parameters documentation. +- [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) Added Nextflow strict syntax compatibility. ### `Changed` -- Updated PR template, PR checklist, feature request template, bug report template and issue template chooser [#24](https://github.com/Clinical-Genomics/oncorefiner/pull/24) -- Updated nf-schema to 2.6.1 [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) -- Updated minimum Nextflow version to 25.10.0 [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) -- Added wgs-cancer-pipeline projects list in the issue templates [#37](https://github.com/Clinical-Genomics/oncorefiner/pull/37) -- Updated documentation [#48](https://github.com/Clinical-Genomics/oncorefiner/pull/48) +- [#24](https://github.com/Clinical-Genomics/oncorefiner/pull/24) Updated PR template, PR checklist, feature request template, bug report template and issue template chooser. +- [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) Updated nf-schema to 2.6.1. +- [#30](https://github.com/Clinical-Genomics/oncorefiner/pull/30) Updated minimum Nextflow version to 25.10.0. +- [#37](https://github.com/Clinical-Genomics/oncorefiner/pull/37) Added wgs-cancer-pipeline projects list in the issue templates. +- [#48](https://github.com/Clinical-Genomics/oncorefiner/pull/48) Updated documentation. ### `Fixed` -- Removed snv_vcf_tbi and sv_vcf_tbi parameter. VCF indexes are now automatically detected [#9](https://github.com/Clinical-Genomics/oncorefiner/pull/9) -- Renamed pipeline from postprocessing to oncorefiner [#10](https://github.com/Clinical-Genomics/oncorefiner/pull/10) -- Fixed linting issues [#20](https://github.com/Clinical-Genomics/oncorefiner/pull/20) -- Fixed nf-test to run a functional default test, and generated a snapshot [#26](https://github.com/Clinical-Genomics/oncorefiner/pull/26) -- Added missing description in bug report template [32](https://github.com/Clinical-Genomics/oncorefiner/pull/32) -- Updated template settings to set organisation to `Clinical-Genomics` and skip unused features `igenomes` and `fastqc` [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) -- Refactored `genome` parameter to have default value 'GRCh38' and no longer refer to igenomes [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) -- Updated linting config to fix linting issues and re-added/removed checks for files where nf-core file structure is no longer required [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) -- Updated template for nf-core/tools version 3.5.2 to apply updated settings and changes missed in previous template update ([#14](https://github.com/Clinical-Genomics/oncorefiner/pull/14)) [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) -- Fixed prepare_references config that was defined but not used [36](https://github.com/Clinical-Genomics/oncorefiner/pull/36) -- Fixed bug and formatting in feature request template [#39](https://github.com/Clinical-Genomics/oncorefiner/pull/39) -- Fixed merge mistake in `.nf-core.yml` introduced in previous PR ([#25](https://github.com/Clinical-Genomics/oncorefiner/pull/25)) [#41](https://github.com/Clinical-Genomics/oncorefiner/pull/41) -- Added necessary GITHUB_TOKEN permissions for action add_pr_checklist_comment [#42](https://github.com/Clinical-Genomics/oncorefiner/pull/42) -- 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) +- [#9](https://github.com/Clinical-Genomics/oncorefiner/pull/9) Removed snv_vcf_tbi and sv_vcf_tbi parameter. VCF indexes are now automatically detected. +- [#10](https://github.com/Clinical-Genomics/oncorefiner/pull/10) Renamed pipeline from postprocessing to oncorefiner. +- [#20](https://github.com/Clinical-Genomics/oncorefiner/pull/20) Fixed linting issues. +- [#26](https://github.com/Clinical-Genomics/oncorefiner/pull/26) Fixed nf-test to run a functional default test, and generated a snapshot. +- [#32](https://github.com/Clinical-Genomics/oncorefiner/pull/32) Added missing description in bug report template. +- [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) Updated template settings to set organisation to `Clinical-Genomics` and skip unused features `igenomes` and `fastqc`. +- [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) Refactored `genome` parameter to have default value 'GRCh38' and no longer refer to igenomes. +- [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) Updated linting config to fix linting issues and re-added/removed checks for files where nf-core file structure is no longer required. +- [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35) Updated template for nf-core/tools version 3.5.2 to apply updated settings and changes missed in previous template update ([#14](https://github.com/Clinical-Genomics/oncorefiner/pull/14)). +- [36](https://github.com/Clinical-Genomics/oncorefiner/pull/36) Fixed prepare_references config that was defined but not used. +- [#39](https://github.com/Clinical-Genomics/oncorefiner/pull/39) Fixed bug and formatting in feature request template. +- [#41](https://github.com/Clinical-Genomics/oncorefiner/pull/41) Fixed merge mistake in `.nf-core.yml` introduced in previous PR ([#25](https://github.com/Clinical-Genomics/oncorefiner/pull/25)). +- [#42](https://github.com/Clinical-Genomics/oncorefiner/pull/42) Added necessary GITHUB_TOKEN permissions for action add_pr_checklist_comment. +- [#34](https://github.com/Clinical-Genomics/oncorefiner/pull/34) Updated all modules and removed deprecated `ch_versions` to implement latest nf-core changes that use the `versions` topic channel to collect software versions. +- [#45](https://github.com/Clinical-Genomics/oncorefiner/pull/45) Fixed settings for `add_pr_checklist_comment` to allow action to run on a PR originated from a fork. ### `Dependencies` @@ -52,4 +52,4 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt ### `Removed` -- Removed CI checks `awstest` and `awsfulltest` [#18](https://github.com/Clinical-Genomics/oncorefiner/pull/18) +- [#18](https://github.com/Clinical-Genomics/oncorefiner/pull/18) Removed CI checks `awstest` and `awsfulltest`. From ede68d27302f9c99af81dc8991446ea9dc13eef6 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 13:33:52 +0100 Subject: [PATCH 17/34] pre-commit to update parameters.md --- docs/parameters.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/parameters.md b/docs/parameters.md index f6a5812..ad0e63f 100644 --- a/docs/parameters.md +++ b/docs/parameters.md @@ -19,9 +19,9 @@ 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 From 75486758e4db640f9b3a01ffdb15951dba444745 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 16:23:47 +0100 Subject: [PATCH 18/34] Add Felix as contributor --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 1b0d862..b1c9e48 100644 --- a/README.md +++ b/README.md @@ -69,7 +69,7 @@ For more details about the output files and reports, please refer to the [output Clinical-Genomics/oncorefiner was originally written by Clinical Genomics Stockholm. -We thank the following people for their extensive assistance in the development of this pipeline: [Eva Caceres](https://github.com/fevac), [Kristine Bilgrav Sæther](https://github.com/kristinebilgrav), [Beatriz Sá Vinhas](https://github.com/beatrizsavinhas) and [Mathias Johansson](https://github.com/mathiasbio). +We thank the following people for their extensive assistance in the development of this pipeline: [Eva Caceres](https://github.com/fevac), [Kristine Bilgrav Sæther](https://github.com/kristinebilgrav), [Beatriz Sá Vinhas](https://github.com/beatrizsavinhas), [Mathias Johansson](https://github.com/mathiasbio) and [Felix Lenner](https://github.com/fellen31). ## Contributions and Support From 068d74d49c3cd6be4eed65a7c1d5fe4a82760d21 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 16:48:38 +0100 Subject: [PATCH 19/34] update README.md usage --- README.md | 31 ++++++++++++++++++------------- 1 file changed, 18 insertions(+), 13 deletions(-) diff --git a/README.md b/README.md index b1c9e48..490a5d7 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,9 @@ # Clinical-Genomics/oncorefiner + + [![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/Clinical-Genomics/oncorefiner) [![GitHub Actions CI Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml) [![GitHub Actions Linting Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) @@ -24,33 +28,28 @@ -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) + + +2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) ## Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - +Each row represents a fastq file (single-end with only `fastq_1`) or a pair of fastq files (paired end with `fastq_1` and `fastq_2`). Now, you can run the pipeline using: - - ```bash nextflow run Clinical-Genomics/oncorefiner \ -profile \ @@ -61,6 +60,8 @@ nextflow run Clinical-Genomics/oncorefiner \ > [!WARNING] > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files). +For more details and further functionality, please refer to the [usage documentation](./docs/usage.md) and the [parameter documentation](./docs/parameters.md). + ## Pipeline output For more details about the output files and reports, please refer to the [output documentation](.github/docs/output.md). @@ -69,7 +70,13 @@ For more details about the output files and reports, please refer to the [output Clinical-Genomics/oncorefiner was originally written by Clinical Genomics Stockholm. -We thank the following people for their extensive assistance in the development of this pipeline: [Eva Caceres](https://github.com/fevac), [Kristine Bilgrav Sæther](https://github.com/kristinebilgrav), [Beatriz Sá Vinhas](https://github.com/beatrizsavinhas), [Mathias Johansson](https://github.com/mathiasbio) and [Felix Lenner](https://github.com/fellen31). +We thank the following people for their extensive assistance in the development of this pipeline: + +- [Eva Caceres](https://github.com/fevac) +- [Kristine Bilgrav Sæther](https://github.com/kristinebilgrav) +- [Beatriz Sá Vinhas](https://github.com/beatrizsavinhas) +- [Mathias Johansson](https://github.com/mathiasbio) +- [Felix Lenner](https://github.com/fellen31) ## Contributions and Support @@ -80,8 +87,6 @@ If you would like to contribute to this pipeline, please see the [contributing g - - An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE). From 17c2903f9d8b6e1d26ecaea6a5bb5b50174c6c2a Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 17:07:03 +0100 Subject: [PATCH 20/34] Fill in introduction in README.md --- README.md | 37 +++++++++++++++++++++++++++++++++++-- 1 file changed, 35 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 490a5d7..1ddbde9 100644 --- a/README.md +++ b/README.md @@ -26,11 +26,44 @@ to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction --> +### Workflow diagram + - -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +1. Process SNV VCF files + 1. Annotate with [`Vcfanno`](https://github.com/brentp/vcfanno) + 1. Filter according to call quality with [`bcftools`](https://github.com/samtools/bcftools) + 1. Filter according to user provided list of research relevant variant with [`bcftools`](https://github.com/samtools/bcftools) + 1. Annotate with [`VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html) + 1. Filter according to user provided list of clinically relevant variants with [`bcftools`](https://github.com/samtools/bcftools) + +1. Process SV VCF files + 1. SVDB QUERY ??? + 1. Filter according to call quality with ??? + 1. Filter according to user provided list of research relevant variant with [`bcftools`](https://github.com/samtools/bcftools) + 1. Annotate with [`VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html) + 1. Filter according to user provided list of clinically relevant variants with [`bcftools`](https://github.com/samtools/bcftools) + +1. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) + +### Summary of tools and version used in the pipeline + +| Step | Tool | Version | +| --------------------- | ------------- | ------- | +| Clinical Filtering | bcftools | 1.22 | +| Clinical Filtering SV | bcftools | 1.22 | +| EnsemblVEP SNV | ensemblvep | 115.2 | +| EnsemblVEP SNV | perl-math-cdf | 0.1 | +| EnsemblVEP SNV | tabix | 1.21 | +| EnsemblVEP SV | ensemblvep | 115.2 | +| EnsemblVEP SV | perl-math-cdf | 0.1 | +| EnsemblVEP SV | tabix | 1.21 | +| Research Filtering | bcftools | 1.22 | +| Research Filtering SV | bcftools | 1.22 | +| SVDB Query DB | svdb | 2.8.4 | +| Untar VEP Cache | untar | 1.34 | +| Vcfanno | vcfanno | 0.3.7 | ## Usage From 3c85e5f78d7c6601ac1011361f127f8b36ce5cbb Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 17:10:01 +0100 Subject: [PATCH 21/34] Add logo code --- README.md | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 1ddbde9..adf8e1c 100644 --- a/README.md +++ b/README.md @@ -1,8 +1,11 @@ # Clinical-Genomics/oncorefiner - +

+ + + nf-core/oncorefiner + +

[![Open in GitHub Codespaces](https://img.shields.io/badge/Open_In_GitHub_Codespaces-black?labelColor=grey&logo=github)](https://github.com/codespaces/new/Clinical-Genomics/oncorefiner) [![GitHub Actions CI Status](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml/badge.svg)](https://github.com/Clinical-Genomics/oncorefiner/actions/workflows/nf-test.yml) From 1b7885e4b4506e08bef876f2d6966d871346a79c Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Mon, 16 Mar 2026 17:10:15 +0100 Subject: [PATCH 22/34] add note to CITATIONS.md --- CITATIONS.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CITATIONS.md b/CITATIONS.md index 2b87728..faaeb18 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,6 +10,8 @@ ## Pipeline tools + + - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. From 0f68e0f7e73e228a4c612e7d1b98aad2ce861569 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 13:12:50 +0100 Subject: [PATCH 23/34] Added introduction to README.md --- README.md | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/README.md b/README.md index adf8e1c..848c1d2 100644 --- a/README.md +++ b/README.md @@ -21,13 +21,7 @@ ## Introduction -**Clinical-Genomics/oncorefiner** is a bioinformatics pipeline that ... - - +**Clinical-Genomics/oncorefiner** is a customizable post-processing and extension layer for Oncoanalyser that adapts its outputs according to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser's robust core. ### Workflow diagram From 5c75381ca8e6f2210675e192baf75b4c23047ed1 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 13:26:53 +0100 Subject: [PATCH 24/34] update citations --- CITATIONS.md | 12 +++++++++++- README.md | 4 ++-- 2 files changed, 13 insertions(+), 3 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index faaeb18..4169c14 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,7 +10,17 @@ ## Pipeline tools - +- [`Vcfanno`](https://github.com/brentp/vcfanno) + +> Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5. PMID: 27250555; PMCID: PMC4888505. + +- [`bcftools`](https://github.com/samtools/bcftools) + +> Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Jan 29;10(2):giab008. doi: 10.1093/gigascience/giab008. PubMed PMID: 33590861; PubMed Central PMCID: PMC7931819. + +- [`Ensembl VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html) + +> McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biology. Jun 6;17(1):122. doi:10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PMCID: PMC4893825. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) diff --git a/README.md b/README.md index 848c1d2..4891199 100644 --- a/README.md +++ b/README.md @@ -32,14 +32,14 @@ 1. Annotate with [`Vcfanno`](https://github.com/brentp/vcfanno) 1. Filter according to call quality with [`bcftools`](https://github.com/samtools/bcftools) 1. Filter according to user provided list of research relevant variant with [`bcftools`](https://github.com/samtools/bcftools) - 1. Annotate with [`VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html) + 1. Annotate with [`Ensembl VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html) 1. Filter according to user provided list of clinically relevant variants with [`bcftools`](https://github.com/samtools/bcftools) 1. Process SV VCF files 1. SVDB QUERY ??? 1. Filter according to call quality with ??? 1. Filter according to user provided list of research relevant variant with [`bcftools`](https://github.com/samtools/bcftools) - 1. Annotate with [`VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html) + 1. Annotate with [`Ensembl VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html) 1. Filter according to user provided list of clinically relevant variants with [`bcftools`](https://github.com/samtools/bcftools) 1. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) From 0ba2b3e61c10cda0f846dc65f0ad2be4f00724a6 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 13:40:22 +0100 Subject: [PATCH 25/34] update usage --- docs/usage.md | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 4e866cb..29cd976 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -4,8 +4,6 @@ ## Introduction - - ## Samplesheet input You will need to create a samplesheet with information about the samples you would like to analyse 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 as shown in the examples below. @@ -14,17 +12,6 @@ You will need to create a samplesheet with information about the samples you wou --input '[path to samplesheet file]' ``` -### Multiple runs of the same sample - -The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: - -```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz -``` - ### Full samplesheet The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below. From 4a899adf94307a54fbf39f4f1ff6500b861e874c Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 13:44:32 +0100 Subject: [PATCH 26/34] update usage --- docs/usage.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/usage.md b/docs/usage.md index 29cd976..227386a 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -56,6 +56,8 @@ work # Directory containing the nextflow working files # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` +Additionally, there are several parameters that can be used to customize the pipeline run. See [parameters documentation](../docs/parameters.md) for a full list of available parameters, their descriptions and formats. + If you wish to repeatedly use the same parameters for multiple runs, rather than specifying each flag in the command, you can specify these in a params file. Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. From 356575d7dda063c3fa9003d4715f36aa638af706 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 14:07:38 +0100 Subject: [PATCH 27/34] Add output example. --- docs/output.md | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/docs/output.md b/docs/output.md index 2447844..0003a76 100644 --- a/docs/output.md +++ b/docs/output.md @@ -6,15 +6,30 @@ This document describes the output produced by the pipeline. Most of the plots a The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. - - ## Pipeline overview The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: + + - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution + + +### Vcfanno + +
+Output files + +- `vcfanno/` + - `SNV_vcfanno.vcf.gz`: a gzipped VCF file containing annotated SNVs. + - `SNV_vcfanno.vcf.gz.tbi`: index file for the gzipped VCF file. + +
+ +[`Vcfanno`](https://github.com/brentp/vcfanno) annotates VCF files with a number of INFO fields from the VCFs or BED files provided. + ### MultiQC
From 4c5204eae48c96c1f3f7d68a7d80d680ad495015 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 14:22:59 +0100 Subject: [PATCH 28/34] update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5c8a5e1..63d7535 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -46,6 +46,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt - [#34](https://github.com/Clinical-Genomics/oncorefiner/pull/34) Updated all modules and removed deprecated `ch_versions` to implement latest nf-core changes that use the `versions` topic channel to collect software versions. - [#45](https://github.com/Clinical-Genomics/oncorefiner/pull/45) Fixed settings for `add_pr_checklist_comment` to allow action to run on a PR originated from a fork. - [#49](https://github.com/Clinical-Genomics/oncorefiner/pull/49) Added `species` parameter to provide information for annotation which was previously hardcoded. +- [#48](https://github.com/Clinical-Genomics/oncorefiner/pull/48) Updated documentation. ### `Dependencies` From efd6985fe396187edd596e6e0132453476eca8cd Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Tue, 17 Mar 2026 14:27:03 +0100 Subject: [PATCH 29/34] update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 81156d1..f51595e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -46,7 +46,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt - [#34](https://github.com/Clinical-Genomics/oncorefiner/pull/34) Updated all modules and removed deprecated `ch_versions` to implement latest nf-core changes that use the `versions` topic channel to collect software versions. - [#45](https://github.com/Clinical-Genomics/oncorefiner/pull/45) Fixed settings for `add_pr_checklist_comment` to allow action to run on a PR originated from a fork. - [#49](https://github.com/Clinical-Genomics/oncorefiner/pull/49) Added `species` parameter to provide information for annotation which was previously hardcoded. -- [#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) Added settings and moved ungrouped parameters to relevant groups. - [#48](https://github.com/Clinical-Genomics/oncorefiner/pull/48) Updated documentation. ### `Dependencies` From de8eb668efb5e7cda1f82f859584e38e1d77444b Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 19 Mar 2026 13:22:48 +0100 Subject: [PATCH 30/34] update ISSUE_TEMPLATE/config --- .github/ISSUE_TEMPLATE/config.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 0086358..d3e657e 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -1 +1,5 @@ blank_issues_enabled: true +contact_links: + - name: Contributing Guidelines + url: https://github.com/Clinical-Genomics/oncorefiner?tab=contributing-ov-file#readme + about: If you would like to contribute to this pipeline, please follow the contributing guidelines. From ed01899be9189d784a086a37c5ccd83a3d37bd24 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Thu, 19 Mar 2026 13:45:19 +0100 Subject: [PATCH 31/34] Update CITATIONS.md --- CITATIONS.md | 24 +++++++++++++----------- 1 file changed, 13 insertions(+), 11 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index 4169c14..e77d8ed 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,30 +1,32 @@ # Clinical-Genomics/oncorefiner: Citations -## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) +## Nextflow & nf-core -> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. +- [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) -## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/) + > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. -> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. +- [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/) -## Pipeline tools - -- [`Vcfanno`](https://github.com/brentp/vcfanno) + > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. -> Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5. PMID: 27250555; PMCID: PMC4888505. +## Pipeline tools - [`bcftools`](https://github.com/samtools/bcftools) -> Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Jan 29;10(2):giab008. doi: 10.1093/gigascience/giab008. PubMed PMID: 33590861; PubMed Central PMCID: PMC7931819. + > Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, Whitwham A, Keane T, McCarthy SA, Davies RM, Li H. Twelve years of SAMtools and BCFtools. Gigascience. 2021 Jan 29;10(2):giab008. doi: 10.1093/gigascience/giab008. PubMed PMID: 33590861; PubMed Central PMCID: PMC7931819. - [`Ensembl VEP`](https://www.ensembl.org/info/docs/tools/vep/index.html) -> McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biology. Jun 6;17(1):122. doi:10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PMCID: PMC4893825. + > McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biology. Jun 6;17(1):122. doi:10.1186/s13059-016-0974-4. PubMed PMID: 27268795; PMCID: PMC4893825. - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) -> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + +- [`Vcfanno`](https://github.com/brentp/vcfanno) + + > Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016 Jun 1;17(1):118. doi: 10.1186/s13059-016-0973-5. PMID: 27250555; PMCID: PMC4888505. ## Software packaging/containerisation tools From 21ca245a899fbf1b2679fe105c36f79b80760db0 Mon Sep 17 00:00:00 2001 From: Beatriz Vinhas Date: Thu, 19 Mar 2026 13:45:53 +0100 Subject: [PATCH 32/34] Update CITATIONS.md --- CITATIONS.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CITATIONS.md b/CITATIONS.md index e77d8ed..4676b71 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -2,14 +2,14 @@ ## Nextflow & nf-core -- [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) - - > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. - - [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/) > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. +- [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) + + > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. + ## Pipeline tools - [`bcftools`](https://github.com/samtools/bcftools) From 913441f84be395edd97fe11930b75efe33bc273b Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Thu, 19 Mar 2026 17:00:39 +0100 Subject: [PATCH 33/34] Move contributing to root directory --- .github/CONTRIBUTING.md => CONTRIBUTING.md | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename .github/CONTRIBUTING.md => CONTRIBUTING.md (100%) diff --git a/.github/CONTRIBUTING.md b/CONTRIBUTING.md similarity index 100% rename from .github/CONTRIBUTING.md rename to CONTRIBUTING.md From 46e2fe050e0a5440f3f229043c77d6992a2785f9 Mon Sep 17 00:00:00 2001 From: beatrizsavinhas Date: Fri, 20 Mar 2026 14:48:44 +0100 Subject: [PATCH 34/34] update docker installation link --- CONTRIBUTING.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 0a2b801..06fbb2a 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -57,7 +57,7 @@ Be positive and constructive in your review, and whenever possible offer suggest In order to run the pipeline, develop and test your changes locally, we recommend that you set up: - A conda environment with `nextflow` and `nf-core` tools. - For this, follow the instructions from the [nf-core documentation](https://nf-co.re/docs/nf-core-tools/installation). Additional information about [Installation of nf-core dependencies](https://nf-co.re/docs/usage/getting_started/installation/) is also available, if needed. -- Install Docker (https://docs.docker.com/engine/install/) and make sure the daemon is running when you want to run the tests locally. +- Install Docker (https://www.docker.com/products/docker-desktop/) and make sure the daemon is running when you want to run the tests locally. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.