Australian-Structural-Biology-Computing · ziadbkh · May 29, 2026 · Aug 12, 2025 · Sep 3, 2025 · Sep 26, 2025
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -7,8 +7,7 @@ body:
       value: |
         Before you post this issue, please check the documentation:
 
-        - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
-        - [nf-core/wisps pipeline documentation](https://nf-co.re/wisps/usage)
+        - [Australian-Structural-Biology-Computing/wisps pipeline documentation](https://nf-co.re/wisps/usage)
 
   - type: textarea
     id: description
@@ -40,11 +39,11 @@ body:
   - type: textarea
     id: system
     attributes:
-      label: System information
+      label: Learn more about contributing
       description: |
         * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * 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/wisps _(eg. 1.1, 1.5, 1.8.2)_
+        * Version of Australian-Structural-Biology-Computing/wisps _(eg. 1.1, 1.5, 1.8.2)_
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -4,4 +4,4 @@ contact_links:
     about: Please join the nf-core community here
   - name: "Slack #wisps channel"
     url: https://nfcore.slack.com/channels/wisps
-    about: Discussion about the nf-core/wisps pipeline
+    about: Discussion about the Australian-Structural-Biology-Computing/wisps pipeline
diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml
@@ -1,5 +1,5 @@
 name: Feature request
-description: Suggest an idea for the nf-core/wisps pipeline
+description: Suggest an idea for the Australian-Structural-Biology-Computing/wisps pipeline
 labels: enhancement
 body:
   - type: textarea

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -1,22 +1,21 @@
 <!--
-# nf-core/wisps pull request
+# Australian-Structural-Biology-Computing/wisps pull request
 
-Many thanks for contributing to nf-core/wisps!
+Many thanks for contributing to Australian-Structural-Biology-Computing/wisps!
 
 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/wisps/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/wisps/tree/master/.github/CONTRIBUTING.md)
-- [ ] If necessary, also make a PR on the nf-core/wisps _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/Australian-Structural-Biology-Computing/wisps/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the Australian-Structural-Biology-Computing/wisps _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>`).

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -15,7 +15,7 @@ jobs:
   run-platform:
     name: Run AWS full tests
     # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
-    if: github.repository == 'nf-core/wisps' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
+    if: github.repository == 'Australian-Structural-Biology-Computing/wisps' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
       - uses: octokit/request-action@v2.x

diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -7,7 +7,7 @@ on:
 jobs:
   run-platform:
     name: Run AWS tests
-    if: github.repository == 'nf-core/wisps'
+    if: github.repository == 'Australian-Structural-Biology-Computing/wisps'
     runs-on: ubuntu-latest
     steps:
       # Launch workflow using Seqera Platform CLI tool action

diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -11,9 +11,9 @@ jobs:
     steps:
       # PRs to the nf-core repo 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/wisps'
+        if: github.repository == 'Australian-Structural-Biology-Computing/wisps'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/wisps ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == Australian-Structural-Biology-Computing/wisps ]] && [[ $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

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -22,7 +22,7 @@ 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/wisps') }}"
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'Australian-Structural-Biology-Computing/wisps') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

diff --git a/.github/workflows/fix-linting.yml b/.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/wisps'
+      github.repository == 'Australian-Structural-Biology-Computing/wisps'
     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/wisps/actions/runs/${{ github.run_id }}) for more details.
+            See [CI log](https://github.com/Australian-Structural-Biology-Computing/wisps/actions/runs/${{ github.run_id }}) for more details.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,23 +1 @@
-bump_version: null
-lint:
-  files_exist:
-  - conf/igenomes.config
-  - conf/igenomes_ignored.config
-  - conf/igenomes.config
-  - conf/igenomes_ignored.config
-nf_core_version: 3.0.2
-org_path: null
 repository_type: pipeline
-template:
-  author: Ziad Al-Bkhetan and Thomas Liftin
-  description: Workflow for Interaction Screening by predicting Structure
-  force: true
-  is_nfcore: true
-  name: wisps
-  org: nf-core
-  outdir: .
-  skip_features:
-  - igenomes
-  - fastqc
-  version: 1.0.0dev
-update: null
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -11,3 +11,8 @@ repos:
     hooks:
       - id: editorconfig-checker
         alias: ec
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,11 +1,11 @@
-# nf-core/wisps: Changelog
+# Australian-Structural-Biology-Computing/wisps: 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]
+## v1.0.0 - [date]
 
-Initial release of nf-core/wisps, created with the [nf-core](https://nf-co.re/) template.
+Initial release of Australian-Structural-Biology-Computing/wisps, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`
 

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -1,4 +1,4 @@
-# nf-core/wisps: Citations
+# Australian-Structural-Biology-Computing/wisps: Citations
 
 ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
 
@@ -10,8 +10,6 @@
 
 ## 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.