Merge pull request #463 from maxulysse/dev_lint

fix: nf-core lint - add dark/light for logos

.github/workflows/ci.yml

@@ -18,10 +18,14 @@ jobs:
       NXF_ANSI_LOG: false
     strategy:
       matrix:
-        # Nextflow versions: check pipeline minimum and latest edge version
-        nxf_ver:
-          - 'NXF_VER=21.10.3'
-        #  - 'NXF_EDGE=1'
+        # Nextflow versions
+        include:
+          # Test pipeline minimum Nextflow version
+          - NXF_VER: '21.10.3'
+            NXF_EDGE: ''
+          # Test latest edge release of Nextflow
+          - NXF_VER: ''
+            NXF_EDGE: '1'
         test:
           - 'aligner'
           - 'annotation'
@@ -39,12 +43,14 @@ jobs:
       - name: Install Nextflow
         env:
           CAPSULE_LOG: none
+          NXF_VER: ${{ matrix.NXF_VER }}
+          # Uncomment only if the edge release is more recent than the latest stable release
+          # See https://github.com/nextflow-io/nextflow/issues/2467
+          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
         run: |
           wget -qO- get.nextflow.io | bash
           sudo mv nextflow /usr/local/bin/
-          export ${{ matrix.nxf_ver }}
           nextflow self-update
-
       - name: Set up Python
         uses: actions/setup-python@v2
         with:

.nf-core.yml

@@ -2,6 +2,7 @@ lint:
   files_unchanged:
     - .github/workflows/linting.yml
     - assets/multiqc_config.yaml
-    - assets/nf-core-sarek_logo.png
-    - docs/images/nf-core-sarek_logo.png
+    - assets/nf-core-sarek_logo_light.png
+    - docs/images/nf-core-sarek_logo_dark.png
+    - docs/images/nf-core-sarek_logo_light.png
     - lib/NfcoreTemplate.groovy

README.md

@@ -1,4 +1,4 @@
-# [![nf-core/sarek](docs/images/nf-core-sarek_logo.png "nf-core/sarek")](https://nf-co.re/sarek)
+# ![nf-core/sarek](docs/images/nf-core-sarek_logo_light.png#gh-light-mode-only) ![nf-core/sarek](docs/images/nf-core-sarek_logo_dark.png#gh-dark-mode-only)
 
 > **An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing**
 

assets/sendmail_template.txt

@@ -12,9 +12,9 @@ $email_html
 Content-Type: image/png;name="nf-core-sarek_logo.png"
 Content-Transfer-Encoding: base64
 Content-ID: <nfcorepipelinelogo>
-Content-Disposition: inline; filename="nf-core-sarek_logo.png"
+Content-Disposition: inline; filename="nf-core-sarek_logo_light.png"
 
-<% out << new File("$projectDir/assets/nf-core-sarek_logo.png").
+<% out << new File("$projectDir/assets/nf-core-sarek_logo_light.png").
     bytes.
     encodeBase64().
     toString().