Merge pull request #310 from danilodileo/template-update3.1.2

Template update3.1.2

.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
@@ -56,37 +67,16 @@ 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
-        run: |
-          nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
-          --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
-          --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
-          --compress "none" \
-          --container-system 'singularity' \
-          --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
-          --container-cache-utilisation 'amend' \
-          --download-configuration 'yes'
-
       - 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 +113,8 @@ 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

@@ -1,4 +1,4 @@
-nf_core_version: 3.1.1
+nf_core_version: 3.1.2
 repository_type: pipeline
 template:
   author: Danilo Di Leo, Emelie Nilsson & Daniel Lundin

CITATIONS.md

@@ -12,7 +12,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 

README.md

@@ -3,7 +3,9 @@
     <source media="(prefers-color-scheme: dark)" srcset="docs/images/nf-core-metatdenovo_logo_dark.png">
     <img alt="nf-core/metatdenovo" src="docs/images/nf-core-metatdenovo_logo_light.png">
   </picture>
-</h1>[![GitHub Actions CI Status](https://github.com/nf-core/metatdenovo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/metatdenovo/actions/workflows/ci.yml)
+</h1>
+
+[![GitHub Actions CI Status](https://github.com/nf-core/metatdenovo/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/metatdenovo/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/metatdenovo/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/metatdenovo/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/metatdenovo/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)
 

docs/usage.md

@@ -239,7 +239,7 @@ nextflow run nf-core/metatdenovo -profile docker -params-file params.yaml
 
 with:
 
-```yaml
+```yaml title="params.yaml"
 input: 'samplesheet.csv'
 assembler: 'spades'
 orf_caller: 'prokka'

modules.json

@@ -32,7 +32,7 @@
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e",
+                        "git_sha": "0e9cb409c32d3ec4f0d3804588e4778971c09b7e",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {