fix lint + modify CI actions

scilus · Dec 20, 2024 · 97d7fbe · 97d7fbe
1 parent cd6db67
commit 97d7fbe
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Showing 4 changed files with 16 additions and 15 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -52,6 +52,11 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+        with:
+          tool-cache: true
+
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
@@ -73,11 +78,6 @@ jobs:
           mkdir -p $NXF_SINGULARITY_CACHEDIR
           mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
-      - name: Clean up Disk space
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
-        with:
-          tool-cache: true
-
       - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
           nf-test test ${GITHUB_WORKSPACE}/tests/${{ matrix.test_name }} --profile ${{ matrix.profile }}
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -8,11 +8,12 @@ lint:
     - .github/ISSUE_TEMPLATE/config.yml
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
-  actions_ci:
-    - .github/workflows/ci.yml
+  actions_ci: False
   files_unchanged:
     - CODE_OF_CONDUCT.md
     - .github/workflows/linting.yml
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
     - assets/nf-core-pediatric_logo_light.png
     - docs/images/nf-core-pediatric_logo_light.png
     - docs/images/nf-core-pediatric_logo_dark.png

diff --git a/assets/multiqc_config_subject.yml → assets/multiqc_config.yml b/assets/multiqc_config_subject.yml → assets/multiqc_config.yml
@@ -4,21 +4,21 @@ report_comment: >
 
 report_section_order:
   "nf-pediatric-summary":
-    order: -600
+    order: -1001
   "shell_qc":
-    order: -650
+    order: -850
   "tissue_segmentation_qc":
-    order: -700
+    order: -600
   "metrics_qc":
-    order: -725
+    order: -625
   "tracking_qc":
-    order: -750
+    order: -650
   "labels_qc":
-    order: -800
+    order: -500
   "nf-pediatric-methods-description":
     order: -900
   software_versions:
-    order: -500
+    order: -1000
 
 custom_content:
   order:

diff --git a/workflows/pediatric.nf b/workflows/pediatric.nf
@@ -615,7 +615,7 @@ workflow PEDIATRIC {
     // MODULE: MultiQC
     //
     ch_multiqc_config_subject = Channel.fromPath(
-        "$projectDir/assets/multiqc_config_subject.yml", checkIfExists: true)
+        "$projectDir/assets/multiqc_config.yml", checkIfExists: true)
     ch_multiqc_config_global = Channel.fromPath(
         "$projectDir/assets/multiqc_config_global.yml", checkIfExists: true)
     ch_multiqc_custom_config = params.multiqc_config ?