Merge branch 'TEMPLATE' of https://github.com/nf-core/smrnaseq into m…

…erging-template-updates-2.3
nf-core · Apr 8, 2022 · 46a9070 · 46a9070
2 parents 7678b60 + 5b7a41b
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diff --git a/.editorconfig b/.editorconfig
@@ -8,12 +8,9 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{yml,yaml}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
-[*.json]
-insert_final_newline = unset
-
 # These files are edited and tested upstream in nf-core/modules
 [/modules/nf-core/**]
 charset = unset

diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -15,8 +15,7 @@ Contributions to the code are even more welcome ;)
 
 If you'd like to write some code for nf-core/smrnaseq, the standard workflow is as follows:
 
-1. Check that there isn't already an issue about your idea in the [nf-core/smrnaseq issues](https://github.com/nf-core/smrnaseq/issues) to avoid duplicating work
-    * If there isn't one already, please create one so that others know you're working on this
+1. Check that there isn't already an issue about your idea in the [nf-core/smrnaseq issues](https://github.com/nf-core/smrnaseq/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/smrnaseq repository](https://github.com/nf-core/smrnaseq) to your GitHub account
 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
@@ -49,9 +48,9 @@ These tests are run both with the latest available version of `Nextflow` and als
 
 :warning: Only in the unlikely and regretful event of a release happening with a bug.
 
-* On your own fork, make a new branch `patch` based on `upstream/master`.
-* Fix the bug, and bump version (X.Y.Z+1).
-* A PR should be made on `master` from patch to directly this particular bug.
+- On your own fork, make a new branch `patch` based on `upstream/master`.
+- Fix the bug, and bump version (X.Y.Z+1).
+- A PR should be made on `master` from patch to directly this particular bug.
 
 ## Getting help
 
@@ -73,7 +72,7 @@ If you wish to contribute a new step, please use the following coding standards:
 6. Add sanity checks and validation for all relevant parameters.
 7. Perform local tests to validate that the new code works as expected.
 8. If applicable, add a new test command in `.github/workflow/ci.yml`.
-9. Update MultiQC config `assets/multiqc_config.yaml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
+9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
 
 ### Default values
@@ -92,8 +91,8 @@ The process resources can be passed on to the tool dynamically within the proces
 
 Please use the following naming schemes, to make it easy to understand what is going where.
 
-* initial process channel: `ch_output_from_<process>`
-* intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
+- initial process channel: `ch_output_from_<process>`
+- intermediate and terminal channels: `ch_<previousprocess>_for_<nextprocess>`
 
 ### Nextflow version bumping
 

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -1,9 +1,7 @@
-
 name: Bug report
 description: Report something that is broken or incorrect
 labels: bug
 body:
-
   - type: markdown
     attributes:
       value: |

diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
@@ -10,16 +10,15 @@ Remember that PRs should be made against the dev branch, unless you're preparing
 
 Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/smrnaseq/tree/master/.github/CONTRIBUTING.md)
 -->
-<!-- markdownlint-disable ul-indent -->
 
 ## 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/smrnaseq/tree/master/.github/CONTRIBUTING.md)
-    - [ ] If necessary, also make a PR on the nf-core/smrnaseq _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/smrnaseq/tree/master/.github/CONTRIBUTING.md)
+  - [ ] If necessary, also make a PR on the nf-core/smrnaseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -14,16 +14,17 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v2
+        uses: nf-core/tower-action@v3
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          pipeline: ${{ github.repository }}
-          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/smrnaseq/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-${{ github.sha }}"
             }
           profiles: test_full,aws_tower
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -10,19 +10,19 @@ jobs:
     if: github.repository == 'nf-core/smrnaseq'
     runs-on: ubuntu-latest
     steps:
+      # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v2
-
+        uses: nf-core/tower-action@v3
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
-          pipeline: ${{ github.repository }}
-          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/smrnaseq/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/smrnaseq/results-test-${{ github.sha }}"
             }
           profiles: test,aws_tower
-
+          nextflow_config: |
+            process.errorStrategy = 'retry'
+            process.maxRetries = 3
diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml
@@ -13,8 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/smrnaseq'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/smrnaseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
-
+          "{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/smrnaseq ]] && [[ $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
@@ -43,4 +42,4 @@ jobs:
             Thanks again for your contribution!
           repo-token: ${{ secrets.GITHUB_TOKEN }}
           allow-repeats: false
-
+#
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -14,20 +14,20 @@ env:
 
 jobs:
   test:
-    name: Run workflow tests
+    name: Run pipeline with test data
     # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/smrnaseq') }}
+    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/smrnaseq') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         # Nextflow versions
         include:
           # Test pipeline minimum Nextflow version
-          - NXF_VER: '21.10.3'
-            NXF_EDGE: ''
+          - NXF_VER: "21.10.3"
+            NXF_EDGE: ""
           # Test latest edge release of Nextflow
-          - NXF_VER: ''
-            NXF_EDGE: '1'
+          - NXF_VER: ""
+            NXF_EDGE: "1"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v2
@@ -44,7 +44,6 @@ jobs:
 
       - name: Run pipeline with test data
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker
-      - name: Run pipeline with test data and not genome
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_no_genome,docker
+          nextflow run ${GITHUB_WORKSPACE} -profile test_no_genome,docker --outdir ./results
+
+#
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -1,44 +1,14 @@
 name: nf-core linting
 # This workflow is triggered on pushes and PRs to the repository.
-# It runs the `nf-core lint` and markdown lint tests to ensure that the code meets the nf-core guidelines
+# It runs the `nf-core lint` and markdown lint tests to ensure
+# that the code meets the nf-core guidelines.
 on:
   push:
   pull_request:
   release:
     types: [published]
 
 jobs:
-  Markdown:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
-      - name: Install markdownlint
-        run: npm install -g markdownlint-cli
-      - name: Run Markdownlint
-        run: markdownlint .
-
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## Markdown linting is failing
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-            * Install `markdownlint-cli`
-                * On Mac: `brew install markdownlint-cli`
-                * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`)
-            * Fix the markdown errors
-                * Automatically: `markdownlint . --fix`
-                * Manually resolve anything left from `markdownlint .`
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-            We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
-
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
@@ -50,42 +20,24 @@ jobs:
         run: npm install -g editorconfig-checker
 
       - name: Run ECLint check
-        run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test)
+        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')
 
-  YAML:
+  Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
+
       - uses: actions/setup-node@v2
-      - name: Install yaml-lint
-        run: npm install -g yaml-lint
-      - name: Run yaml-lint
-        run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") -c ${GITHUB_WORKSPACE}/.markdownlint.yml
 
-      # If the above check failed, post a comment on the PR explaining the failure
-      - name: Post PR comment
-        if: failure()
-        uses: mshick/add-pr-comment@v1
-        with:
-          message: |
-            ## YAML linting is failing
-            To keep the code consistent with lots of contributors, we run automated code consistency checks.
-            To fix this CI test, please run:
-            * Install `yaml-lint`
-                * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`)
-            * Fix the markdown errors
-                * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")`
-                * Fix any reported errors in your YAML files
-            Once you push these changes the test should pass, and you can hide this comment :+1:
-            We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!
-            Thanks again for your contribution!
-          repo-token: ${{ secrets.GITHUB_TOKEN }}
-          allow-repeats: false
+      - name: Install Prettier
+        run: npm install -g prettier
+
+      - name: Run Prettier --check
+        run: prettier --check ${GITHUB_WORKSPACE}
 
   nf-core:
     runs-on: ubuntu-latest
     steps:
-
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
@@ -97,8 +49,8 @@ jobs:
           sudo mv nextflow /usr/local/bin/
       - uses: actions/setup-python@v1
         with:
-          python-version: '3.6'
-          architecture: 'x64'
+          python-version: "3.6"
+          architecture: "x64"
 
       - name: Install dependencies
         run: |
@@ -124,3 +76,5 @@ jobs:
             lint_log.txt
             lint_results.md
             PR_number.txt
+
+#
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -1,4 +1,3 @@
-
 name: nf-core linting comment
 # This workflow is triggered after the linting action is complete
 # It posts an automated comment to the PR, even if the PR is coming from a fork
@@ -27,4 +26,4 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}
           path: linting-logs/lint_results.md
-
+#
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -0,0 +1,14 @@
+image: nfcore/gitpod:latest
+
+vscode:
+  extensions: # based on nf-core.nf-core-extensionpack
+    - codezombiech.gitignore # Language support for .gitignore files
+    # - cssho.vscode-svgviewer                 # SVG viewer
+    - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
+    # - nextflow.nextflow                      # Nextflow syntax highlighting
+    - oderwat.indent-rainbow # Highlight indentation level
+    - streetsidesoftware.code-spell-checker # Spelling checker for source code
diff --git a/.markdownlint.yml b/.markdownlint.yml
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,3 +1,4 @@
+repository_type: pipeline
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md

diff --git a/.prettierrc.yml b/.prettierrc.yml
@@ -0,0 +1 @@
+printWidth: 120
diff --git a/CITATIONS.md b/CITATIONS.md
@@ -10,7 +10,7 @@
 
 ## Pipeline tools
 
-* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 * [trimgalore](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
 
@@ -36,16 +36,19 @@
 
 ## Software packaging/containerisation tools
 
-* [Anaconda](https://anaconda.com)
-    > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+- [Anaconda](https://anaconda.com)
 
-* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
-    > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
 
-* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
-    > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
 
-* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+  > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
 
-* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
-    > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
+- [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+
+  > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+
+- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+
+- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+  > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.