Template update to v3.2.1 (#37)

* Template update for nf-core/tools version 3.1.1

* template update

* Template update for nf-core/tools version 3.2.1

* changelog

* changelog prettier

Author: famosab

.github/workflows/download_pipeline.yml

@@ -29,7 +29,7 @@ env:
 
 jobs:
   configure:
-    runs-on: ubuntu-latest{% raw %}
+    runs-on: ubuntu-latest
     outputs:
       REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
       REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
@@ -40,7 +40,7 @@ jobs:
         run: |
           echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT{% endraw %}"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
 
   download:
     runs-on: ubuntu-latest
@@ -85,10 +85,10 @@ jobs:
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}{% endraw %}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
 
       - name: Inspect container images
-        run: tree ./singularity_container_images | tee ./container_initial{% if test_config %}{% raw %}
+        run: tree ./singularity_container_images | tee ./container_initial
 
       - name: Count the downloaded number of container images
         id: count_initial

.nf-core.yml

@@ -27,7 +27,7 @@ lint:
   nextflow_config:
     - manifest.name
     - manifest.homePage
-nf_core_version: 3.2.0
+nf_core_version: 3.2.1
 repository_type: pipeline
 template:
   author: SusiJo, FriederikeHanssen, famosab

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [#34](https://github.com/qbic-pipelines/vcftomaf/pull/34) - Update vcf2maf configuration to adhere to hg38 as reference genome (@famosab)
 - [#35](https://github.com/qbic-pipelines/vcftomaf/pull/35) - Template update to 3.2.0 (@famosab)
+- [#37](https://github.com/qbic-pipelines/vcftomaf/pull/37) - Template update to 3.2.1 (@famosab)
 
 ### `Dependencies`
 

docs/output.md

@@ -70,7 +70,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 [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>

nextflow.config

@@ -264,7 +264,7 @@ manifest {
 
 // Nextflow plugins
 plugins {
-    id 'nf-schema@2.3.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
+    id 'nf-schema@2.2.0' // Validation of pipeline parameters and creation of an input channel from a sample sheet
 }
 
 validation {