Add example samplesheet with differen file endings for pipeline mspepid

.github/renovate.json5

@@ -0,0 +1,5 @@
+{
+  $schema: "https://docs.renovatebot.com/renovate-schema.json",
+  extends: ["github>nf-core/ops//.github/renovate/default.json5"],
+  baseBranchPatterns: ["master"],
+}

.github/workflows/fix-linting.yml

@@ -0,0 +1,82 @@
+name: Fix linting from a comment
+on:
+  issue_comment:
+    types: [created]
+
+jobs:
+  fix-linting:
+    # Only run if comment is on a PR with the main repo, and if it contains the magic keywords
+    if: >
+      contains(github.event.comment.html_url, '/pull/') &&
+      contains(github.event.comment.body, '@nf-core-bot fix linting') &&
+      github.repository == 'nf-core/test-datasets'
+    runs-on: ubuntu-latest
+    steps:
+      # Use the @nf-core-bot token to check out so we can push later
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+        with:
+          token: ${{ secrets.nf_core_bot_auth_token }}
+
+      # indication that the linting is being fixed
+      - name: React on comment
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: eyes
+
+      # Action runs on the issue comment, so we don't get the PR by default
+      # Use the gh cli to check out the PR
+      - name: Checkout Pull Request
+        run: gh pr checkout ${{ github.event.issue.number }}
+        env:
+          GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
+
+      # Install and run prek
+      - name: Run prek
+        id: prek
+        uses: j178/prek-action@91fd7d7cf70ae1dee9f4f44e7dfa5d1073fe6623 # v1
+        continue-on-error: true
+
+      # indication that the linting has finished
+      - name: react if linting finished succesfully
+        if: steps.prek.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: "+1"
+
+      - name: Commit & push changes
+        id: commit-and-push
+        if: steps.prek.outcome == 'failure'
+        run: |
+          git config user.email "core@nf-co.re"
+          git config user.name "nf-core-bot"
+          git config push.default upstream
+          git add .
+          git status
+          git commit -m "[automated] Fix code linting"
+          git push
+
+      - name: react if linting errors were fixed
+        id: react-if-fixed
+        if: steps.commit-and-push.outcome == 'success'
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: hooray
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome == 'failure'
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
+        with:
+          comment-id: ${{ github.event.comment.id }}
+          reactions: confused
+
+      - name: react if linting errors were not fixed
+        if: steps.commit-and-push.outcome  == 'failure'
+        uses: peter-evans/create-or-update-comment@e8674b075228eee787fea43ef493e45ece1004c9 # v5
+        with:
+          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/test-datasets/actions/runs/${{ github.run_id }}) for more details.

.github/workflows/lint-code.yml

@@ -0,0 +1,20 @@
+name: Run pre-commit hooks
+on:
+  push:
+    branches:
+      - "**" # runs on all branches
+
+# Cancel if a newer run is started
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6
+
+      - name: Run prek
+        uses: j178/prek-action@91fd7d7cf70ae1dee9f4f44e7dfa5d1073fe6623 # v1

.pre-commit-config.yaml

@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - prettier@3.7.1
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+        args:
+          - --markdown-linebreak-ext=md
+      - id: end-of-file-fixer
+  - repo: local
+    hooks:
+      - id: prevent-file-deletion
+        name: Prevent file deletions
+        language: system
+        entry: bash -c 'git diff --cached --name-only --diff-filter=D | grep -q . && echo "❌ File deletions are not allowed. Ask on slack for exceptions" && exit 1 || exit 0'
+        pass_filenames: false

README.md

@@ -1,4 +1,5 @@
 # ![nfcore/test-datasets](docs/images/test-datasets_logo.png)
+
 Test data to be used for automated testing with the nf-core pipelines
 
 > ⚠️ **Do not merge your test data to `master`! Each pipeline has a dedicated branch (and a special one for modules)**
@@ -13,8 +14,8 @@ The principle for nf-core test data is as small as possible, as large as necessa
 
 nf-core/test-datasets comes with documentation in the `docs/` directory:
 
-01. [Add a new  test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md)
-02. [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
+1.  [Add a new test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/ADD_NEW_DATA.md)
+2.  [Use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
 
 ## Downloading test data
 

docs/ADD_NEW_DATA.md

@@ -2,13 +2,13 @@
 
 Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested when adding a new test dataset.
 
- - [ ] Check [here](https://github.com/nf-core/test-datasets/branches/all) that there isn't already a branch containing data that could be used
-   - If this is the case, follow the [documentation on how to use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
- - [ ] Fork the [nf-core/test-datasets repository](https://github.com/nf-core/test-datasets) to your GitHub account
- - [ ] Create a new branch on your fork
- - [ ] Check your proposed test data follows the [guidelines](https://nf-co.re/docs/contributing/test_data_guidelines)
- - [ ] Add your test dataset
-   - [ ] If you clone it locally use `git clone <url> --branch <branch> --single-branch`
- - [ ] Make a PR on a new branch with a relevant name
- - [ ] Wait for the PR to be merged
- - [ ] Use this newly created branch for your tests
+- [ ] Check [here](https://github.com/nf-core/test-datasets/branches/all) that there isn't already a branch containing data that could be used
+  - If this is the case, follow the [documentation on how to use an existing test dataset](https://github.com/nf-core/test-datasets/blob/master/docs/USE_EXISTING_DATA.md)
+- [ ] Fork the [nf-core/test-datasets repository](https://github.com/nf-core/test-datasets) to your GitHub account
+- [ ] Create a new branch on your fork
+- [ ] Check your proposed test data follows the [guidelines](https://nf-co.re/docs/contributing/test_data_guidelines)
+- [ ] Add your test dataset
+  - [ ] If you clone it locally use `git clone <url> --branch <branch> --single-branch`
+- [ ] Make a PR on a new branch with a relevant name
+- [ ] Wait for the PR to be merged
+- [ ] Use this newly created branch for your tests

docs/USE_EXISTING_DATA.md

@@ -2,10 +2,10 @@
 
 Please fill in the appropriate checklist below (delete whatever is not relevant). These are the most common things requested when adding a new test dataset.
 
- - [ ] Check [here](https://github.com/nf-core/test-datasets/branches/all) to find the branch corresponding to the test dataset you want to use (i.e., `modules`, or a given pipeline)
-   - [ ] Alternatively use nf-core tools to search and explore, e.g. `nf-core test-datasets list` (press tab for options), and then `nf-core test-datasets search -b modules fasta` (press tab for options)
-   - [ ] You can also use the flag `--generate-nf-path` to generate config ready strings
- - [ ] Specify in the `conf/test.config` the path to the files from the test dataset 
- - [ ] Set up your CI tests following the nf-core best practices
-   - [ ] For pipelines: [tests/default.nf.test](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/tests/default.nf.test))
-   - [ ] For modules: [tests/main.nf.test](https://github.com/nf-core/tools/blob/main/nf_core/module-template/tests/main.nf.test.j2)
+- [ ] Check [here](https://github.com/nf-core/test-datasets/branches/all) to find the branch corresponding to the test dataset you want to use (i.e., `modules`, or a given pipeline)
+  - [ ] Alternatively use nf-core tools to search and explore, e.g. `nf-core test-datasets list` (press tab for options), and then `nf-core test-datasets search -b modules fasta` (press tab for options)
+  - [ ] You can also use the flag `--generate-nf-path` to generate config ready strings
+- [ ] Specify in the `conf/test.config` the path to the files from the test dataset
+- [ ] Set up your CI tests following the nf-core best practices
+  - [ ] For pipelines: [tests/default.nf.test](https://github.com/nf-core/tools/blob/main/nf_core/pipeline-template/tests/default.nf.test))
+  - [ ] For modules: [tests/main.nf.test](https://github.com/nf-core/tools/blob/main/nf_core/module-template/tests/main.nf.test.j2)

example_samplesheet.csv

@@ -0,0 +1,9 @@
+ID,spectrum_file
+1,/yourDirectory/sample1.d
+2,/yourDirectory/sample2.tar.gz
+3,/yourDirectory/sample3.zip
+4,/yourDirectory/sample4.raw
+5,/yourDirectory/sample5.raw.gz
+6,/yourDirectory/sample6.raw.tar.gz
+7,/yourDirectory/sample7.raw.zip
+8,/yourDirectory/sample8.raw