fix: change name from postprocessing to oncorefiner

.github/CONTRIBUTING.md

@@ -1,20 +1,20 @@
-# `nf-core/postprocessing`: Contributing Guidelines
+# `nf-core/oncorefiner`: Contributing Guidelines
 
 Hi there!
-Many thanks for taking an interest in improving nf-core/postprocessing.
+Many thanks for taking an interest in improving nf-core/oncorefiner.
 
-We try to manage the required tasks for nf-core/postprocessing using GitHub issues, you probably came to this page when creating one.
+We try to manage the required tasks for nf-core/oncorefiner using GitHub issues, you probably came to this page when creating one.
 Please use the pre-filled template to save time.
 
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
 ## Contribution workflow
 
-If you'd like to write some code for nf-core/postprocessing, the standard workflow is as follows:
+If you'd like to write some code for nf-core/oncorefiner, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/postprocessing issues](https://github.com/nf-core/postprocessing/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
-2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/postprocessing repository](https://github.com/nf-core/postprocessing) to your GitHub account
+1. Check that there isn't already an issue about your idea in the [nf-core/oncorefiner issues](https://github.com/nf-core/oncorefiner/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this
+2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/oncorefiner repository](https://github.com/nf-core/oncorefiner) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core pipelines schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
@@ -58,11 +58,11 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 ## Getting help
 
-For further information/help, please consult the [nf-core/postprocessing documentation](https://nf-co.re/postprocessing/usage) and don't hesitate to get in touch on the nf-core Slack [#postprocessing](https://nfcore.slack.com/channels/postprocessing) channel ([join our Slack here](https://nf-co.re/join/slack)).
+For further information/help, please consult the [nf-core/oncorefiner documentation](https://nf-co.re/oncorefiner/usage) and don't hesitate to get in touch on the nf-core Slack [#oncorefiner](https://nfcore.slack.com/channels/oncorefiner) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Pipeline contribution conventions
 
-To make the `nf-core/postprocessing` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
+To make the `nf-core/oncorefiner` code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.
 
 ### Adding a new step
 
@@ -112,7 +112,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes
 
 To get started:
 
-- Open the repo in [Codespaces](https://github.com/nf-core/postprocessing/codespaces)
+- Open the repo in [Codespaces](https://github.com/nf-core/oncorefiner/codespaces)
 - Tools installed
   - nf-core
   - Nextflow

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -8,7 +8,7 @@ body:
         Before you post this issue, please check the documentation:
 
         - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/postprocessing pipeline documentation](https://nf-co.re/postprocessing/usage)
+        - [nf-core/oncorefiner pipeline documentation](https://nf-co.re/oncorefiner/usage)
   - type: textarea
     id: description
     attributes:
@@ -46,4 +46,4 @@ body:
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
-        * Version of nf-core/postprocessing _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of nf-core/oncorefiner _(eg. 1.1, 1.5, 1.8.2)_

.github/ISSUE_TEMPLATE/config.yml

@@ -2,6 +2,6 @@ contact_links:
   - name: Join nf-core
     url: https://nf-co.re/join
     about: Please join the nf-core community here
-  - name: "Slack #postprocessing channel"
-    url: https://nfcore.slack.com/channels/postprocessing
-    about: Discussion about the nf-core/postprocessing pipeline
+  - name: "Slack #oncorefiner channel"
+    url: https://nfcore.slack.com/channels/oncorefiner
+    about: Discussion about the nf-core/oncorefiner pipeline

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/postprocessing pipeline
+description: Suggest an idea for the nf-core/oncorefiner pipeline
 labels: enhancement
 body:
   - type: textarea

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,22 +1,22 @@
 <!--
-# nf-core/postprocessing pull request
+# nf-core/oncorefiner pull request
 
-Many thanks for contributing to nf-core/postprocessing!
+Many thanks for contributing to nf-core/oncorefiner!
 
 Please fill in the appropriate checklist below (delete whatever is not relevant).
 These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/postprocessing/tree/master/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/oncorefiner/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/postprocessing/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/postprocessing _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/oncorefiner/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/oncorefiner _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).

.github/workflows/awsfulltest.yml

@@ -14,7 +14,7 @@ jobs:
   run-platform:
     name: Run AWS full tests
     # run only if the PR is approved by at least 2 reviewers and against the master/main branch or manually triggered
-    if: github.repository == 'nf-core/postprocessing' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
+    if: github.repository == 'nf-core/oncorefiner' && github.event.review.state == 'approved' && (github.event.pull_request.base.ref == 'master' || github.event.pull_request.base.ref == 'main') || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - name: Set revision variable
@@ -32,11 +32,11 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           revision: ${{ steps.revision.outputs.revision }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/postprocessing/work-${{ steps.revision.outputs.revision }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/oncorefiner/work-${{ steps.revision.outputs.revision }}
           parameters: |
             {
               "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/postprocessing/results-${{ steps.revision.outputs.revision }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/oncorefiner/results-${{ steps.revision.outputs.revision }}"
             }
           profiles: test_full
 

.github/workflows/awstest.yml

@@ -7,7 +7,7 @@ on:
 jobs:
   run-platform:
     name: Run AWS tests
-    if: github.repository == 'nf-core/postprocessing'
+    if: github.repository == 'nf-core/oncorefiner'
     runs-on: ubuntu-latest
     steps:
       # Launch workflow using Seqera Platform CLI tool action
@@ -18,10 +18,10 @@ jobs:
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
           revision: ${{ github.sha }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/postprocessing/work-${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/oncorefiner/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/postprocessing/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/oncorefiner/results-test-${{ github.sha }}"
             }
           profiles: test
 

.github/workflows/branch.yml

@@ -13,9 +13,9 @@ jobs:
     steps:
       # PRs to the nf-core repo main/master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches
       - name: Check PRs
-        if: github.repository == 'nf-core/postprocessing'
+        if: github.repository == 'nf-core/oncorefiner'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/postprocessing ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/oncorefiner ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/ci.yml

@@ -22,17 +22,14 @@ jobs:
   test:
     name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/postprocessing') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/oncorefiner') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
-          - "24.04.2"
-          - "latest-everything"
+          - "25.10.3"
         profile:
-          - "conda"
           - "docker"
-          - "singularity"
         test_name:
           - "test"
         isMaster:

.github/workflows/fix-linting.yml

@@ -9,7 +9,7 @@ jobs:
     if: >
       contains(github.event.comment.html_url, '/pull/') &&
       contains(github.event.comment.body, '@nf-core-bot fix linting') &&
-      github.repository == 'nf-core/postprocessing'
+      github.repository == 'nf-core/oncorefiner'
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
@@ -86,4 +86,4 @@ jobs:
           issue-number: ${{ github.event.issue.number }}
           body: |
             @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually.
-            See [CI log](https://github.com/nf-core/postprocessing/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/nf-core/oncorefiner/actions/runs/${{ github.run_id }}) for more details.

.nf-core.yml

@@ -6,7 +6,7 @@ lint: {}
 
 template:
   org: nf-core
-  name: postprocessing
+  name: oncorefiner
   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

CHANGELOG.md

@@ -1,24 +1,25 @@
-# nf-core/postprocessing: Changelog
+# nf-core/oncorefiner: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## v1.0.0dev - [date]
 
-Initial release of nf-core/postprocessing, created with the [nf-core](https://nf-co.re/) template.
+Initial release of nf-core/oncorefiner, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 
-- Added Ensembl VEP annotation for SNV vcf file [#1](https://github.com/Clinical-Genomics/nf-core-postprocessing/pull/1)
-- Added VCFANNO annotation for SNV vcf file [#2](https://github.com/Clinical-Genomics/nf-core-postprocessing/pull/2)
-- Added filtering for SNV vcf file [#3](https://github.com/Clinical-Genomics/nf-core-postprocessing/pull/3)
-- Added annotation for SV vcf file [#4](https://github.com/Clinical-Genomics/nf-core-postprocessing/pull/4)
-- Added filtering for SV vcf file [#5](https://github.com/Clinical-Genomics/nf-core-postprocessing/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/nf-core-postprocessing/pull/8)
+- 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)
 
 ### `Fixed`
 
-- Removed snv_vcf_tbi and sv_vcf_tbi parameter. VCF indexes are now automatically detected [#9](https://github.com/Clinical-Genomics/nf-core-postprocessing/pull/9)
+- 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 []()
 
 ### `Dependencies`
 

CITATIONS.md

@@ -1,4 +1,4 @@
-# nf-core/postprocessing: Citations
+# nf-core/oncorefiner: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) The nf-core/postprocessing team
+Copyright (c) The nf-core/oncorefiner team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal