Important! Template update for nf-core/tools v2.13

.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/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

@@ -106,10 +106,10 @@ jobs:
 
     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: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
         with:
           version: "${{ matrix.NXF_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
@@ -23,13 +28,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # 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: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # 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(.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/[email protected]
+      - 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 }}!

.nf-core.yml

@@ -3,8 +3,5 @@ lint:
   actions_ci: false
   files_exist:
     - conf/modules.config
-    - lib/NfcoreTemplate.groovy
-    - lib/Utils.groovy
-    - lib/WorkflowMain.groovy
   files_unchanged:
     - assets/sendmail_template.txt

CHANGELOG.md

@@ -47,6 +47,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #266](https://github.com/nf-core/fetchngs/pull/266) - Make .gitignore match template
 - [PR #268](https://github.com/nf-core/fetchngs/pull/268) - Add mermaid diagram
 - [PR #273](https://github.com/nf-core/fetchngs/pull/273) - Update utility subworkflows
+- [PR #283](https://github.com/nf-core/fetchngs/pull/283) - Template update for nf-core/tools v2.13
 
 ### Software dependencies
 

README.md

@@ -5,17 +5,14 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/fetchngs/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/fetchngs/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/fetchngs/results)
-[![nf-test](https://img.shields.io/badge/tested_with-nf--test-337ab7.svg)](https://github.com/askimed/nf-test)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)
+[![GitHub Actions CI Status](https://github.com/nf-core/fetchngs/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/fetchngs/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/fetchngs/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/fetchngs/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/fetchngs/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.5070524-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.5070524)[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](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)](https://tower.nf/launch?pipeline=https://github.com/nf-core/fetchngs)
+[![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/fetchngs)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23fetchngs-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/fetchngs)[![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)
 

main.nf

@@ -13,11 +13,19 @@ nextflow.enable.dsl = 2
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOWS FOR PIPELINE
+    IMPORT FUNCTIONS / MODULES / SUBWORKFLOWS / WORKFLOWS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { SRA } from './workflows/sra'
+include { SRA                     } from './workflows/sra'
+include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_fetchngs_pipeline'
+include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_fetchngs_pipeline'
+
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    NAMED WORKFLOWS FOR PIPELINE
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
 
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
@@ -38,16 +46,10 @@ workflow NFCORE_FETCHNGS {
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN ALL WORKFLOWS
+    RUN MAIN WORKFLOW
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_fetchngs_pipeline'
-include { PIPELINE_COMPLETION     } from './subworkflows/local/utils_nfcore_fetchngs_pipeline'
-
-//
-// WORKFLOW: Execute a single named workflow for the pipeline
-//
 workflow {
 
     //
@@ -58,6 +60,7 @@ workflow {
         params.help,
         params.validate_params,
         params.monochrome_logs,
+        args,
         params.outdir,
         params.input,
         params.ena_metadata_fields

nextflow_schema.json

@@ -16,9 +16,9 @@
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
+                    "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.(csv|tsv|txt)$",
-                    "schema": "assets/schema_input.json",
                     "fa_icon": "fas fa-file-excel",
                     "description": "File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files."
                 },

pyproject.toml

@@ -3,11 +3,13 @@
 [tool.ruff]
 line-length = 120
 target-version = "py38"
-select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
 cache-dir = "~/.cache/ruff"
 
-[tool.ruff.isort]
+[tool.ruff.lint]
+select = ["I", "E1", "E4", "E7", "E9", "F", "UP", "N"]
+
+[tool.ruff.lint.isort]
 known-first-party = ["nf_core"]
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "__init__.py" = ["E402", "F401"]

subworkflows/local/utils_nfcore_fetchngs_pipeline/main.nf

@@ -33,6 +33,7 @@ workflow PIPELINE_INITIALISATION {
     help                // boolean: Display help text
     validate_params     // boolean: Boolean whether to validate parameters against the schema at runtime
     monochrome_logs     // boolean: Do not use coloured log outputs
+    nextflow_cli_args   //   array: List of positional nextflow CLI args
     outdir              //  string: The output directory where the results will be saved
     input               //  string: File containing SRA/ENA/GEO/DDBJ identifiers one per line to download their associated metadata and FastQ files
     ena_metadata_fields //  string: Comma-separated list of ENA metadata fields to fetch before downloading data
@@ -52,8 +53,8 @@ workflow PIPELINE_INITIALISATION {
     //
     // Validate parameters and generate parameter summary to stdout
     //
-    def pre_help_text = nfCoreLogo(monochrome_logs)
-    def post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
+    pre_help_text = nfCoreLogo(monochrome_logs)
+    post_help_text = '\n' + workflowCitation() + '\n' + dashedLine(monochrome_logs)
     def String workflow_command = "nextflow run ${workflow.manifest.name} -profile <docker/singularity/.../institute> --input ids.csv --outdir <OUTDIR>"
     UTILS_NFVALIDATION_PLUGIN (
         help,
@@ -67,7 +68,9 @@ workflow PIPELINE_INITIALISATION {
     //
     // Check config provided to the pipeline
     //
-    UTILS_NFCORE_PIPELINE ( args )
+    UTILS_NFCORE_PIPELINE (
+        nextflow_cli_args
+    )
 
     //
     // Auto-detect input id type

subworkflows/local/utils_nfcore_fetchngs_pipeline/tests/main.workflow_pipeline_initialisation.nf.test

@@ -17,16 +17,18 @@ nextflow_workflow {
                 help                = false
                 validate_params     = false
                 monochrome_logs     = false
+                nextflow_cli_args   = []
                 outdir              = "$params.outdir"
                 ena_metadata_fields = null
 
                 input[0] = version
                 input[1] = help
                 input[2] = validate_params
                 input[3] = monochrome_logs
-                input[4] = outdir
-                input[5] = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
-                input[6] = ena_metadata_fields
+                input[4] = nextflow_cli_args
+                input[5] = outdir
+                input[6] = 'https://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv'
+                input[7] = ena_metadata_fields
                 """
             }
         }