Template update for nf-core/tools version 3.1.2

.github/PULL_REQUEST_TEMPLATE.md

@@ -8,14 +8,14 @@ These are the most common things requested on pull requests (PRs).
 
 Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
 
-Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mag/tree/main/.github/CONTRIBUTING.md)
+Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md)
 -->
 
 ## PR checklist
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/main/.github/CONTRIBUTING.md)
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/mag/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/mag _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core pipelines lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).

.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

@@ -1,11 +1,11 @@
 lint:
   files_unchanged:
-  - lib/NfcoreTemplate.groovy
+    - lib/NfcoreTemplate.groovy
   nextflow_config:
-  - config_defaults:
-    - params.phix_reference
-    - params.lambda_reference
-nf_core_version: 3.1.1
+    - config_defaults:
+        - params.phix_reference
+        - params.lambda_reference
+nf_core_version: 3.1.2
 repository_type: pipeline
 template:
   author: "Hadrien Gourl\xE9, Daniel Straub, Sabrina Krakau, James A. Fellows Yates,\
@@ -16,4 +16,4 @@ template:
   name: mag
   org: nf-core
   outdir: .
-  version: 3.3.0
+  version: 3.3.1dev

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v3.3.0 - [date]
+## v3.3.1dev - [date]
 
 Initial release of nf-core/mag, created with the [nf-core](https://nf-co.re/) template.
 

CITATIONS.md

@@ -12,7 +12,9 @@
 
 - [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].
+
+- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
 > 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-mag_logo_dark.png">
     <img alt="nf-core/mag" src="docs/images/nf-core-mag_logo_light.png">
   </picture>
-</h1>[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml)
+</h1>
+
+[![GitHub Actions CI Status](https://github.com/nf-core/mag/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/mag/actions/workflows/ci.yml)
 [![GitHub Actions Linting Status](https://github.com/nf-core/mag/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/mag/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/mag/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)
 
@@ -32,7 +34,7 @@
 ## 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.
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -89,7 +91,9 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 ## Citations
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use nf-core/mag for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) --><!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+<!-- If you use nf-core/mag for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+
+<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/3.3.0" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/tree/dev" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/3.3.0/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000

assets/schema_input.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/mag/main/assets/schema_input.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/mag/master/assets/schema_input.json",
     "title": "nf-core/mag pipeline - params.input schema",
     "description": "Schema for the file provided with params.input",
     "type": "array",

nextflow.config

@@ -273,15 +273,15 @@ manifest {
     homePage        = 'https://github.com/nf-core/mag'
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
-    defaultBranch   = 'main'
+    defaultBranch   = 'master'
     nextflowVersion = '!>=24.04.2'
-    version         = '3.3.0'
+    version         = '3.3.1dev'
     doi             = ''
 }
 
 // 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 {
@@ -307,7 +307,7 @@ validation {
     https://doi.org/10.1038/s41587-020-0439-x
 
 * Software dependencies
-    https://github.com/nf-core/mag/blob/main/CITATIONS.md
+    https://github.com/nf-core/mag/blob/master/CITATIONS.md
 """
     }
     summary {

nextflow_schema.json

@@ -1,6 +1,6 @@
 {
     "$schema": "https://json-schema.org/draft/2020-12/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/mag/main/nextflow_schema.json",
+    "$id": "https://raw.githubusercontent.com/nf-core/mag/master/nextflow_schema.json",
     "title": "nf-core/mag pipeline parameters",
     "description": "Assembly, binning and annotation of metagenomes",
     "type": "object",