Clinical-Genomics · beatrizsavinhas · Mar 12, 2026 · Mar 12, 2026 · Mar 12, 2026 · Mar 12, 2026
@@ -21,6 +21,46 @@ 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 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
+
+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:
+
+- 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:
@@ -98,6 +138,13 @@ 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]`
 
+### Update nf-core 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).

@@ -14,15 +14,15 @@ lint:
     - .prettierignore
     - assets/sendmail_template.txt
     - docs/README.md
+    - .github/CONTRIBUTING.md
   multiqc_config: false
 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

@@ -9,47 +9,48 @@ 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)
-
-### 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)
+- [#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`
+
+- [#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 []()
-- 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)
-- 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 introduced in [#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)
-- Added `species` parameter to provide information for annotation which was previously hardcoded [#49](https://github.com/Clinical-Genomics/oncorefiner/pull/49)
+- [#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.
+- [#49](https://github.com/Clinical-Genomics/oncorefiner/pull/49) Added `species` parameter to provide information for annotation which was previously hardcoded.
 
 ### `Dependencies`
 
 ### `Deprecated`
 
 ### `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`.
@@ -1,5 +1,9 @@
 # Clinical-Genomics/oncorefiner
 
+<!-- TODO:
+   Add logo here.
+-->
+
 [![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 @@
 
 <!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
      workflows use the "tube map" design for that. See https://nf-co.re/docs/guidelines/graphic_design/workflow_diagrams#examples for examples.   -->
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+
+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.
 
-<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
-     Explain what rows and columns represent. For instance (please edit as appropriate):
-
 First, prepare a samplesheet with your input data that looks as follows:
 
 `samplesheet.csv`:
 
 ```csv
 sample,fastq_1,fastq_2
-CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+SAMPLE_ID,SAMPLE_ID_S1_L002_R1_001.fastq.gz,SAMPLE_ID_S1_L002_R2_001.fastq.gz
 ```
 
-Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
-
--->
+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:
 
-<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
-
 ```bash
 nextflow run Clinical-Genomics/oncorefiner \
    -profile <docker/singularity/.../institute> \
@@ -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)
+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
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use Clinical-Genomics/oncorefiner for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 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).