Update template 2.13.1

.devcontainer/devcontainer.json

@@ -10,15 +10,7 @@
         "vscode": {
             // Set *default* container specific settings.json values on container create.
             "settings": {
-                "python.defaultInterpreterPath": "/opt/conda/bin/python",
-                "python.linting.enabled": true,
-                "python.linting.pylintEnabled": true,
-                "python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
-                "python.formatting.yapfPath": "/opt/conda/bin/yapf",
-                "python.linting.flake8Path": "/opt/conda/bin/flake8",
-                "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
-                "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.defaultInterpreterPath": "/opt/conda/bin/python"
             },
 
             // Add the IDs of extensions you want installed when the container is created.

.editorconfig

@@ -18,7 +18,12 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-indent_size = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
 
 [/assets/email*]
 indent_size = unset
@@ -28,5 +33,5 @@ indent_size = unset
 indent_style = unset
 
 # ignore python
-[*.{py}]
+[*.{py,md}]
 indent_style = unset

.github/CONTRIBUTING.md

@@ -9,9 +9,8 @@ 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 ;)
 
-:::info
-If you need help using or modifying nf-core/ampliseq then the best place to ask is on the nf-core Slack [#ampliseq](https://nfcore.slack.com/channels/ampliseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
-:::
+> [!NOTE]
+> If you need help using or modifying nf-core/ampliseq then the best place to ask is on the nf-core Slack [#ampliseq](https://nfcore.slack.com/channels/ampliseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
 
 ## Contribution workflow
 
@@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
-You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
-receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+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:
+
+```bash
+nf-test test --profile debug,test,docker --verbose
+```
 
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
@@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.
 
 Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.
 
-The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
+The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.
 
 ### Naming schemes
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/ampl
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/ampliseq/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/ampliseq _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 --outdir <OUTDIR>`).
+- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/branch.yml

@@ -19,7 +19,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v2
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:

.github/workflows/ci.yml

@@ -63,7 +63,7 @@ jobs:
 
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Check out test data
         uses: actions/checkout@v3
@@ -87,6 +87,9 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Install nf-test
         run: |
           wget -qO- https://code.askimed.com/install/nf-test | bash -s $NFTEST_VER

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v9
+      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/download_pipeline.yml

@@ -6,6 +6,11 @@ name: Test successful pipeline download with 'nf-core download'
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
+    inputs:
+      testbranch:
+        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        required: true
+        default: "dev"
   pull_request:
     types:
       - opened
@@ -25,11 +30,11 @@ jobs:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.11"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@v7
+      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
           singularity-version: 3.8.3
 
@@ -42,13 +47,13 @@ jobs:
         run: |
           echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
       - name: Download the pipeline
         env:
           NXF_SINGULARITY_CACHEDIR: ./
         run: |
-          nf-core download  ${{ env.REPO_LOWERCASE }} \
+          nf-core download ${{ env.REPO_LOWERCASE }} \
           --revision ${{ env.REPO_BRANCH }} \
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \

.github/workflows/linting.yml

@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
           cache: "pip"
@@ -32,12 +32,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.11"
           architecture: "x64"
@@ -60,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v3
+        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@v2
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.github/workflows/release-announcements.yml

@@ -9,6 +9,11 @@ jobs:
   toot:
     runs-on: ubuntu-latest
     steps:
+      - name: get topics and convert to hashtags
+        id: get_topics
+        run: |
+          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -20,11 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
+            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -56,7 +63,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/bluesky-post-action@v0.1.0
+      - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

.gitpod.yml

@@ -10,13 +10,11 @@ tasks:
 
 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
+    # - nextflow.nextflow                    # Nextflow syntax highlighting
     - oderwat.indent-rainbow # Highlight indentation level
     - streetsidesoftware.code-spell-checker # Spelling checker for source code
+    - charliermarsh.ruff # Code linter Ruff

CHANGELOG.md

@@ -14,7 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#697](https://github.com/nf-core/ampliseq/pull/697),[#699](https://github.com/nf-core/ampliseq/pull/699) - Template update for nf-core/tools version 2.12
+- [#697](https://github.com/nf-core/ampliseq/pull/697),[#699](https://github.com/nf-core/ampliseq/pull/699),[#713](https://github.com/nf-core/ampliseq/pull/713) - Template update for nf-core/tools version 2.13.1
 
 ### `Dependencies`
 

README.md

@@ -5,17 +5,16 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/ampliseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/ampliseq/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/ampliseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/ampliseq/actions?query=workflow%3A%22nf-core+linting%22)
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/ampliseq/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1493841-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1493841)
-[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-important?labelColor=000000)](https://doi.org/10.3389/fmicb.2020.550420)
+[![GitHub Actions CI Status](https://github.com/nf-core/ampliseq/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/ampliseq/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/ampliseq/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/ampliseq/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/ampliseq/results)[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
+
+[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1493841-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1493841)[![Cite Publication](https://img.shields.io/badge/Cite%20Us!-Cite%20Publication-important?labelColor=000000)](https://doi.org/10.3389/fmicb.2020.550420)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg?labelColor=000000)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7?labelColor=000000)](https://tower.nf/launch?pipeline=https://github.com/nf-core/ampliseq)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/ampliseq)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23ampliseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/ampliseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)[![Watch on YouTube](http://img.shields.io/badge/youtube-ampliseq-FFFF00?labelColor=000000&logo=youtube)](https://youtu.be/a0VOEeAvETs)
 

assets/multiqc_config.yml

@@ -11,3 +11,9 @@ report_section_order:
     order: -1002
 
 export_plots: true
+
+disable_version_detection: true
+
+# MultiQC version 1.20 & 1.21 need that flag to produce plots!
+# TODO: Remove with version greater than 1.21!
+plots_force_flat: true

conf/modules.config

@@ -415,7 +415,6 @@ process {
         ]
     }
 
-
     withName: BARRNAP {
         ext.kingdom = "bac,arc,mito,euk"
         ext.args = "--quiet --reject 0.1"

conf/test_iontorrent.config

@@ -22,9 +22,12 @@ params {
     // Input data
     FW_primer = "GTGARTCATCGARTCTTTG"
     RV_primer = "TCCTCSSCTTATTGATATGC"
-    dada_ref_taxonomy = "unite-fungi=8.3"
+    sintax_ref_taxonomy = "unite-fungi=8.2"
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet_it_SE_ITS.tsv"
     iontorrent = true
     max_ee = 5
     skip_qiime = true
+
+    // Prevent default taxonomic classification
+    skip_dada_taxonomy = true
 }

conf/test_pacbio_its.config

@@ -12,7 +12,7 @@
 
 params {
     config_profile_name = 'Test profile PacBio ITS'
-    config_profile_description = 'Minimal test dataset to check pipeline function with PacBio ITS sequences and options --cut_its (set to "full") and --addsh enabled'
+    config_profile_description = 'Minimal test dataset to check pipeline function with PacBio ITS sequences and options --cut_its (set to "full")'
 
     // Limit resources so that this can run on GitHub Actions
     max_cpus   = 2
@@ -22,13 +22,16 @@ params {
     // Input data
     FW_primer = "CTTGGTCATTTAGAGGAAGTAA"
     RV_primer = "TCCTGAGGGAAACTTCG"
-    dada_ref_taxonomy = "unite-fungi=8.3"
+    sintax_ref_taxonomy = "unite-fungi=8.2"
     input = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Samplesheet_pacbio_ITS.tsv"
     metadata = "https://raw.githubusercontent.com/nf-core/test-datasets/ampliseq/samplesheets/Metadata_pacbio_ITS.tsv"
     pacbio = true
     max_ee = 12
     cut_its = "full"
-    addsh = true
+    // addsh = true
     skip_qiime = true
     sbdiexport = true
+
+    // Prevent default taxonomic classification
+    skip_dada_taxonomy = true
 }