Merge pull request #20 from nf-core/nf-core-template-merge-2.14.1

Important! Template update for nf-core/tools v2.14.1

.editorconfig

@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset

.github/PULL_REQUEST_TEMPLATE.md

@@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/scna
 - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/scnanoseq/tree/master/.github/CONTRIBUTING.md)
 - [ ] If necessary, also make a PR on the nf-core/scnanoseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
-- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
+- [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.

.github/workflows/awsfulltest.yml

@@ -8,12 +8,12 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/scnanoseq'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -30,7 +30,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json

.github/workflows/awstest.yml

@@ -5,13 +5,13 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/scnanoseq'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json

.github/workflows/ci.yml

@@ -29,10 +29,10 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 

.github/workflows/download_pipeline.yml

@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,11 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -65,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
         run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

.github/workflows/linting.yml

@@ -15,13 +15,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -33,14 +32,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -61,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

.github/workflows/release-announcements.yml

@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,13 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies

.nf-core.yml

@@ -1,4 +1,5 @@
 repository_type: pipeline
+nf_core_version: "2.14.1"
 
 pipeline_todos: false
 

.pre-commit-config.yaml

@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - [email protected]
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:

CITATIONS.md

@@ -50,7 +50,7 @@
 
 - [ToulligQC](https://github.com/GenomiqueENS/toulligQC)
 
-  >Karine Dias, Bérengère Laffay, Lionel Ferrato-Berberian, Sophie Lemoine, Ali Hamraoui, Morgane Thomas-Chollier, Stéphane Le Crom and Laurent Jourdren.
+  > Karine Dias, Bérengère Laffay, Lionel Ferrato-Berberian, Sophie Lemoine, Ali Hamraoui, Morgane Thomas-Chollier, Stéphane Le Crom and Laurent Jourdren.
 
 - [UMI-tools](https://pubmed.ncbi.nlm.nih.gov/28100584/)
 

README.md

@@ -13,7 +13,7 @@
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/scnanoseq)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/scnanoseq)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23scnanoseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/scnanoseq)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 
@@ -29,7 +29,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ![scnanoseq diagram](assets/scnanoseq_diagram.png)
 
-1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [`NanoPlot`](https://github.com/wdecoster/NanoPlot),  [`NanoComp`](https://github.com/wdecoster/nanocomp) and [`ToulligQC`](https://github.com/GenomiqueENS/toulligQC))
+1. Raw read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [`NanoPlot`](https://github.com/wdecoster/NanoPlot), [`NanoComp`](https://github.com/wdecoster/nanocomp) and [`ToulligQC`](https://github.com/GenomiqueENS/toulligQC))
 2. Unzip and split FastQ ([`gunzip`](https://linux.die.net/man/1/gunzip))
    1. Optional: Split fastq for faster processing ([`split`](https://linux.die.net/man/1/split))
 3. Trim and filter reads. ([`Nanofilt`](https://github.com/wdecoster/nanofilt))
@@ -41,11 +41,8 @@ On release, automated continuous integration tests run the pipeline on a full-si
 7. Barcode correction (custom script `./bin/correct_barcodes.py`)
 8. Post-extraction QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [`NanoPlot`](https://github.com/wdecoster/NanoPlot) and [`ToulligQC`](https://github.com/GenomiqueENS/toulligQC))
 9. Alignment ([`minimap2`](https://github.com/lh3/minimap2))
-10. SAMtools processing including ([`SAMtools`](http://www.htslib.org/doc/samtools.html)):
-   1. SAM to BAM
-   2. Filtering of mapped only reads
-   3. Sorting, indexing and obtain mapping metrics
-11. Post-mapping QC in unfiltered BAM files ([`NanoComp`](https://github.com/wdecoster/nanocomp), [`RSeQC`](https://rseqc.sourceforge.net/))
+10. Post-alignment filtering of mapped reads and gathering mapping QC ([`SAMtools`](http://www.htslib.org/doc/samtools.html))
+11. Post-alignment QC in unfiltered BAM files ([`NanoComp`](https://github.com/wdecoster/nanocomp), [`RSeQC`](https://rseqc.sourceforge.net/))
 12. Barcode tagging with read quality, BC, BC quality, UMI, and UMI quality (custom script `./bin/tag_barcodes.py`)
 13. UMI-based deduplication [`UMI-tools`](https://github.com/CGATOxford/UMI-tools)
 14. Gene and transcript level matrices generation. [`IsoQuant`](https://github.com/ablab/IsoQuant)
@@ -110,9 +107,9 @@ If you experience any issues, please make sure to submit an issue above. However
 process
 {
     withName: '.*:.*FASTQC.*'
-    {   
+    {
         cpus = 20
-    }   
+    }
 }
 
 //NOTE: reminder that params set in modules.config need to be copied over to a custom config

assets/multiqc_config.yml

@@ -57,8 +57,7 @@ top_modules:
 custom_content:
   read_counts_section:
     parent_id: read_counts_section
-    order:
-        read_counts_module
+    order: read_counts_module
 
   seurat_section:
     parent_id: seurat_section
@@ -74,7 +73,7 @@ custom_data:
     section_name: "Read Counts"
     file_format: "csv"
     plot_type: "table"
-  
+
   gene_seurat_stats_module:
     parent_id: seurat_section
     parent_name: "Seurat Section"

bin/config.py

@@ -15,7 +15,7 @@
 ADPT_MAC_MATCH_ED=2 #minimum proportion of match required when searching
 
 ## format suffix
-SEQ_SUFFIX_WIN=200 
+SEQ_SUFFIX_WIN=200
 SEQ_SUFFIX_MIN_MATCH_PROP=1
 SEQ_SUFFIX_AFT_ADPT=(20,50)
 
@@ -61,13 +61,12 @@ def high_sensitivity_threshold_calculation(count_array, exp_cells):
 DEFAULT_BC_STAT_FN = "summary.txt"
 DEFAULT_EMPTY_DROP_MIN_ED = 5 # minimum edit distance from emtpy drop BC to selected BC
 DEFAULT_EMPTY_DROP_NUM = 2000 # number of BC in the output
-
 
 ####################################################
 #####    DEFAULT in Demultiplexing            ######
 ####################################################
 
-DEFAULT_ASSIGNMENT_ED = 2 
+DEFAULT_ASSIGNMENT_ED = 2
 # Make sure this is smaller than DEFAULT_GRB_FLANKING_SIZE
 assert DEFAULT_GRB_FLANKING_SIZE >= DEFAULT_ASSIGNMENT_ED
 DEFAULT_ED_FLANKING = DEFAULT_ASSIGNMENT_ED