Merge pull request #20 from nf-core/nf-core-template-merge-3.2.0

Important! Template update for nf-core/tools v3.2.0
nf-core · Jan 29, 2025 · 9f502d6 · 9f502d6
2 parents 3f276ec + f24c762
commit 9f502d6
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Showing 9 changed files with 50 additions and 86 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -46,6 +46,8 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
+        with:
+          fetch-depth: 0
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -34,6 +34,17 @@ jobs:
       REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
       REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
       REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
+    steps:
+      - name: Get the repository name and current branch
+        id: get_repo_properties
+        run: |
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
+
+  download:
+    runs-on: ubuntu-latest
+    needs: configure
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -56,21 +67,10 @@ jobs:
           python -m pip install --upgrade pip
           pip install git+https://github.com/nf-core/tools.git@dev
 
-      - name: Get the repository name and current branch set as environment variable
-        id: get_repo_properties
-        run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
-
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
 
-  download:
-    runs-on: ubuntu-latest
-    needs: configure
-    steps:
       - name: Download the pipeline
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
@@ -87,6 +87,9 @@ jobs:
       - name: Inspect download
         run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
 
+      - name: Inspect container images
+        run: tree ./singularity_container_images | tee ./container_initial
+
       - name: Count the downloaded number of container images
         id: count_initial
         run: |
@@ -123,7 +126,8 @@ jobs:
             final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
-            tree ./singularity_container_images
+            tree ./singularity_container_images > ./container_afterwards
+            diff ./container_initial ./container_afterwards
             exit 1
           else
             echo "The pipeline can be downloaded successfully!"

diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@80620a5d27ce0ae443b965134db88467fc607b43 # v7
+        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
         with:
           workflow: linting.yml
           workflow_conclusion: completed

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -27,39 +27,6 @@ jobs:
 
             ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
-  send-tweet:
-    runs-on: ubuntu-latest
-
-    steps:
-      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
-        with:
-          python-version: "3.10"
-      - name: Install dependencies
-        run: pip install tweepy==4.14.0
-      - name: Send tweet
-        shell: python
-        run: |
-          import os
-          import tweepy
-
-          client = tweepy.Client(
-              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
-              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
-              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
-              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
-          )
-          tweet = os.getenv("TWEET")
-          client.create_tweet(text=tweet)
-        env:
-          TWEET: |
-            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
-            Please see the changelog: ${{ github.event.release.html_url }}
-          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
-          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
-          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
-          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
-
   bsky-post:
     runs-on: ubuntu-latest
     steps:

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -9,7 +9,7 @@ lint:
   multiqc_config: false
   nextflow_config:
     - params.input
-nf_core_version: 3.1.1
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: Judith Bernett

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -7,7 +7,7 @@ repos:
           - [email protected]
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec
diff --git a/README.md b/README.md
@@ -3,7 +3,9 @@
     <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-drugresponseeval_logo_dark.png">
     <img alt="nf-core/drugresponseeval" src="docs/images/nf-core-drugresponseeval_logo_light.png">
   </picture>
-</h1>[![GitHub Actions CI Status](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml)
+</h1>
+
+[![GitHub Actions CI Status](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/drugresponseeval/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/drugresponseeval/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/drugresponseeval/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
@@ -49,7 +51,7 @@ For baseline models, no randomization or robustness tests are performed.
 ## Usage
 
 > [!NOTE]
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
+> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.
 
 Now, you can run the pipeline using:
 
@@ -95,7 +97,9 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 ## Citations
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/drugresponseeval for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --><!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+<!-- If you use nf-core/drugresponseeval for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+
+<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

diff --git a/nextflow.config b/nextflow.config
@@ -202,14 +202,14 @@ env {
 }
 
 // Set bash options
-process.shell = """\
-bash
-
-set -e # Exit if a tool returns a non-zero status/exit code
-set -u # Treat unset variables and parameters as an error
-set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
-set -C # No clobber - prevent output redirection from overwriting files.
-"""
+process.shell = [
+    "bash",
+    "-C",         // No clobber - prevent output redirection from overwriting files.
+    "-e",         // Exit if a tool returns a non-zero status/exit code
+    "-u",         // Treat unset variables and parameters as an error
+    "-o",         // Returns the status of the last command to exit..
+    "pipefail"    //   ..with a non-zero status or zero if all successfully execute
+]
 
 // Disable process selector warnings by default. Use debug profile to enable warnings.
 nextflow.enable.configProcessNamesValidation = false
@@ -256,7 +256,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.1.1' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {