Merge pull request #356 from jonasscheid/merge-template-320

Merge template 3.2.0
nf-core · Jan 28, 2025 · 52215de · 52215de
2 parents 9a7ab01 + 7a72b5f
commit 52215de
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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
@@ -1,7 +1,7 @@
 lint:
   files_unchanged:
     - .github/CONTRIBUTING.md
-nf_core_version: 3.1.2
+nf_core_version: 3.2.0
 repository_type: pipeline
 template:
   author: Jonas Scheid, Steffen Lemke, Leon Bichmann, Marissa Dubbelaar

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/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Template update 3.0.2 [#337](https://github.com/nf-core/mhcquant/pull/337)
 - Template update 3.1.1 [#346](https://github.com/nf-core/mhcquant/pull/346)
 - Template update 3.1.2 [#354](https://github.com/nf-core/mhcquant/pull/354)
+- Template update 3.2.0 [#356](https://github.com/nf-core/mhcquant/pull/356)
 
 ### `Dependencies`
 

diff --git a/docs/output.md b/docs/output.md
@@ -116,7 +116,9 @@ This folder contains the intermediate results from various steps of the MHCquant
 
 [MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory.
 
-Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.### Pipeline information
+Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.
+
+### Pipeline information
 
 <details markdown="1">
 <summary>Output files</summary>

diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
diff --git a/nextflow.config b/nextflow.config
@@ -257,7 +257,8 @@ process.shell = [
     "-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 pipefail" // Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
+    "-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.

diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json
@@ -99,7 +99,7 @@
             },
             "mentions": [
                 {
-                    "@id": "#1379486e-73e5-4aa7-8c2c-39c609f02e3a"
+                    "@id": "#bd6cdd85-ff1c-410c-813d-e8cbc9a05ec5"
                 }
             ],
             "name": "nf-core/mhcquant"
@@ -124,17 +124,17 @@
             "@type": ["File", "SoftwareSourceCode", "ComputationalWorkflow"],
             "creator": [
                 {
-                    "@id": "https://orcid.org/0000-0002-8937-3457"
+                    "@id": "https://orcid.org/0000-0001-7135-0073"
                 },
                 {
-                    "@id": "https://orcid.org/0000-0001-7135-0073"
+                    "@id": "https://orcid.org/0000-0002-8937-3457"
                 },
                 {
                     "@id": "https://orcid.org/0000-0002-6503-2180"
                 }
             ],
             "dateCreated": "",
-            "dateModified": "2025-01-20T14:34:38Z",
+            "dateModified": "2025-01-27T14:47:42Z",
             "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/",
             "keywords": [
                 "nf-core",
@@ -180,11 +180,11 @@
             "version": "!>=24.04.2"
         },
         {
-            "@id": "#1379486e-73e5-4aa7-8c2c-39c609f02e3a",
+            "@id": "#bd6cdd85-ff1c-410c-813d-e8cbc9a05ec5",
             "@type": "TestSuite",
             "instance": [
                 {
-                    "@id": "#60b229d8-92e4-4c50-a90e-59aadb3ec356"
+                    "@id": "#441804d3-a007-4dc5-a5eb-80d9b16c39f5"
                 }
             ],
             "mainEntity": {
@@ -193,7 +193,7 @@
             "name": "Test suite for nf-core/mhcquant"
         },
         {
-            "@id": "#60b229d8-92e4-4c50-a90e-59aadb3ec356",
+            "@id": "#441804d3-a007-4dc5-a5eb-80d9b16c39f5",
             "@type": "TestInstance",
             "name": "GitHub Actions workflow for testing nf-core/mhcquant",
             "resource": "repos/nf-core/mhcquant/actions/workflows/ci.yml",
@@ -321,18 +321,18 @@
             "name": "nf-core",
             "url": "https://nf-co.re/"
         },
-        {
-            "@id": "https://orcid.org/0000-0002-8937-3457",
-            "@type": "Person",
-            "email": "[email protected]",
-            "name": "Lukas Heumos"
-        },
         {
             "@id": "https://orcid.org/0000-0001-7135-0073",
             "@type": "Person",
             "email": "[email protected]",
             "name": "Leon Bichmann"
         },
+        {
+            "@id": "https://orcid.org/0000-0002-8937-3457",
+            "@type": "Person",
+            "email": "[email protected]",
+            "name": "Lukas Heumos"
+        },
         {
             "@id": "https://orcid.org/0000-0002-6503-2180",
             "@type": "Person",