Merge pull request #231 from heuermh/merging-template-updates

Merging template updates for 3.1.2

.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

.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!"

.nf-core.yml

@@ -3,7 +3,7 @@ lint:
     - assets/nf-core-pangenome_logo_light.png
     - docs/images/nf-core-pangenome_logo_light.png
     - docs/images/nf-core-pangenome_logo_dark.png
-nf_core_version: 3.1.1
+nf_core_version: 3.1.2
 repository_type: pipeline
 template:
   author: Simon Heumos, Michael L Heuer
@@ -17,7 +17,7 @@ template:
   name: pangenome
   org: nf-core
   outdir: .
-  version: 1.2.0dev
   skip_features:
     - fastqc
     - igenomes
+  version: 1.2.0dev

README.md

@@ -40,7 +40,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 ## 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:
 

nextflow.config

@@ -303,7 +303,7 @@ 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 {

subworkflows/local/utils_nfcore_pangenome_pipeline/main.nf

@@ -153,31 +153,6 @@ def validateInputParameters() {
     }
 }
 
-//
-// Get attribute from genome config file e.g. fasta
-//
-def getGenomeAttribute(attribute) {
-    if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
-        if (params.genomes[ params.genome ].containsKey(attribute)) {
-            return params.genomes[ params.genome ][ attribute ]
-        }
-    }
-    return null
-}
-
-//
-// Exit pipeline if incorrect --genome key provided
-//
-def genomeExistsError() {
-    if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
-        def error_string = "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" +
-            "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
-            "  Currently, the available genome keys are:\n" +
-            "  ${params.genomes.keySet().join(", ")}\n" +
-            "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~"
-        error(error_string)
-    }
-}
 //
 // Generate methods description for MultiQC
 //

workflows/pangenome.nf

@@ -3,7 +3,6 @@
     IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
-
 include { paramsSummaryMap       } from 'plugin/nf-schema'
 include { paramsSummaryMultiqc   } from '../subworkflows/nf-core/utils_nfcore_pipeline'
 include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline'