Merge branch 'dev' into nf-core-template-merge-2.14.1

.github/workflows/awsfulltest.yml

@@ -12,12 +12,12 @@ jobs:
     name: Run AWS full tests
     if: github.repository == 'nf-core/scrnaseq'
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        aligner: ["alevin", "kallisto", "star", "cellranger", "universc"]
     steps:
       - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
-        # Add full size test data (but still relatively small datasets for few samples)
-        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}

.github/workflows/awstest.yml

@@ -9,6 +9,9 @@ jobs:
     name: Run AWS tests
     if: github.repository == 'nf-core/scrnaseq'
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        aligner: ["alevin", "kallisto", "star", "cellranger", "universc"]
     steps:
       # Launch workflow using Seqera Platform CLI tool action
       - name: Launch workflow via Seqera Platform
@@ -21,7 +24,8 @@ jobs:
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/scrnaseq/work-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/scrnaseq/results-test-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/scrnaseq/results-test-${{ github.sha }}/aligner_${{ matrix.aligner }}",
+              "aligner": "${{ matrix.aligner }}"
             }
           profiles: test
 

.github/workflows/ci.yml

@@ -1,32 +1,44 @@
-name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
+name: nf-core CI
 on:
   push:
     branches:
       - dev
   pull_request:
   release:
     types: [published]
+  merge_group:
+    types:
+      - checks_requested
+    branches:
+      - master
+      - dev
 
 env:
   NXF_ANSI_LOG: false
+  NFTEST_VER: "0.8.1"
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
   test:
-    name: Run pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
+    name: "aligner: ${{ matrix.profile }} ; NF: ${{ matrix.NXF_VER }}"
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/scrnaseq') }}"
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
         NXF_VER:
           - "23.04.0"
           - "latest-everything"
+        profile: ["alevin", "cellranger", "kallisto", "star"]
+
     steps:
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
@@ -35,12 +47,33 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+      - name: Cache nf-test installation
+        id: cache-software
+        uses: actions/cache@v3
+        with:
+          path: |
+            /usr/local/bin/nf-test
+            /home/runner/.nf-test/nf-test.jar
+          key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest
+
+      - name: Install nf-test
+        if: steps.cache-software.outputs.cache-hit != 'true'
+        run: |
+          wget -qO- https://code.askimed.com/install/nf-test | bash
+          sudo mv nf-test /usr/local/bin/
 
-      - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
-        # For example: adding multiple test runs with different parameters
-        # Remember that you can parallelise this by using strategy.matrix
+      - name: Run nf-test
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nf-test test tests/main_pipeline_${{ matrix.profile }}.test --junitxml=test.xml
+
+      - name: Output log on failure
+        if: failure()
+        run: |
+          sudo apt install bat > /dev/null
+          batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log
+
+      - name: Publish Test Report
+        uses: mikepenz/action-junit-report@v3
+        if: always() # always run even if the previous step fails
+        with:
+          report_paths: test.xml

.github/workflows/download_pipeline.yml

@@ -29,6 +29,9 @@ jobs:
   download:
     runs-on: ubuntu-latest
     steps:
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
 

.gitignore

@@ -6,3 +6,8 @@ results/
 testing/
 testing*
 *.pyc
+log/
+reports/
+testme.sh
+.nf-test*
+.vscode

.nf-core.yml

@@ -1,2 +1,11 @@
 repository_type: pipeline
 nf_core_version: "2.14.1"
+lint:
+  template_strings: False
+  files_unchanged:
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+  files_exist:
+    - lib/Utils.groovy
+  # TODO This is because of an issue with the monochromeLogs parameter
+  # See nextflow.config for details
+  schema_params: False

CHANGELOG.md

@@ -3,14 +3,121 @@
 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).
 
-## v2.6.0 - [date]
+## v2.6.0 - 2024-04-16
 
-Initial release of nf-core/scrnaseq, created with the [nf-core](https://nf-co.re/) template.
+- Update cellranger to v8.0.0 ([#317](https://github.com/nf-core/scrnaseq/pull/317))
+- Change from pytests to nf-test ([#291](https://github.com/nf-core/scrnaseq/pull/291))
+- Update template to v2.13.1 ([#309](https://github.com/nf-core/scrnaseq/pull/309))
+- Update to kallisto|bustools v0.28.2 ([#294](https://github.com/nf-core/scrnaseq/pull/294))
+- Fix cellrangerarc matrix conversions and protocol selection ([#300](https://github.com/nf-core/scrnaseq/pull/300))
+- Add new emptydrops calling module ([#301](https://github.com/nf-core/scrnaseq/pull/301))
+- Update cellranger modules to latest version ([[#316](https://github.com/nf-core/scrnaseq/issues/316)])
 
-### `Added`
+## v2.5.1 - 2024-01-23
 
-### `Fixed`
+- Template update to v2.12 ([#298](https://github.com/nf-core/scrnaseq/pull/298)).
+- Fix that cellranger workflow couldn't be run and enable CI for this workflow ([#288](https://github.com/nf-core/scrnaseq/pull/288)).
+- Update modules ([#288]()https://github.com/nf-core/scrnaseq/pull/288).
 
-### `Dependencies`
+## v2.5.0 - 2024-01-02
 
-### `Deprecated`
+- Update template to v2.11.1 ([#279](https://github.com/nf-core/scrnaseq/pull/279))
+- Add support for paired GEX+ATAC sequencing using cellranger-arc ([#274](https://github.com/nf-core/scrnaseq/pull/274))
+- Increase default runtime limits for some processes ([#281](https://github.com/nf-core/scrnaseq/pull/281), [#284](https://github.com/nf-core/scrnaseq/pull/284))
+- Better support for custom protocols ([#273](https://github.com/nf-core/scrnaseq/pull/273)).
+  - The universc protocol is now specified via the `--protocol` flag
+  - Any protocol specified is now passed to the respective aligner
+  - Added a section to the documentation
+
+## v2.4.1 - 2023-09-28
+
+- Fix whitelist logic for dropseq ([#267](https://github.com/nf-core/scrnaseq/pull/267))
+- Fix false-positive filename check in cellranger module ([#261](https://github.com/nf-core/scrnaseq/pull/261))
+- Template update to v2.10 ([#269](https://github.com/nf-core/scrnaseq/pull/269))
+
+## v2.4.0 - 2023-08-16 Lime Platinum Crab
+
+- Fix typo causing empty version imformation for mtx_conversion subworkflow ([#254](https://github.com/nf-core/scrnaseq/pull/254))
+- Add `singularity.registry = 'quay.io'` and bump NF version to 23.04.0 ([#237](https://github.com/nf-core/scrnaseq/pull/237))
+- Fixed issue with file collisions while using cellranger ([#232](https://github.com/nf-core/scrnaseq/pull/232))
+- Fix issue where multiqc inputs tried to access objects that did not exist ([#239](https://github.com/nf-core/scrnaseq/pull/239))
+- Removed `public_aws_ecr` profile ([#242](https://github.com/nf-core/scrnaseq/pull/242))
+- Include cellranger in MultiQC report ([#244](https://github.com/nf-core/scrnaseq/pull/244))
+- Nf-core template update to v2.9 ([#245](https://github.com/nf-core/scrnaseq/pull/245))
+- Update cellranger and fastqc module ([#246](https://github.com/nf-core/scrnaseq/pull/246)).
+  The [updated cellranger module](https://github.com/nf-core/modules/pull/3537) now automatically renames input FASTQ
+  files to match the expected naming conventions.
+
+## v2.3.2 - 2023-06-07 Sepia Samarium Salmon
+
+- Move containers for pipeline to quay.io ([#233](https://github.com/nf-core/scrnaseq/pull/233))
+
+## v2.3.1 - 2023-06-02 Yellow Strontium Pinscher
+
+- Add `public_aws_ecr` config for using the AWS mirror of containers where possible ([#225](https://github.com/nf-core/scrnaseq/pull/225))
+
+## v2.3.0 Steelblue Waspaloy Dachshund
+
+- Fix problem on samplesheet check related to amount of columns ([[#211](https://github.com/nf-core/scrnaseq/issues/211)])
+- Fixed bug in starsolo output cardinality.
+
+## v2.2.0
+
+- Added support to output 10x count files in text format.
+- Add gene symbols to count matrices
+- Added UniverSC aligner to implement open-source version of Cell Ranger with wrapper for 40 technologies
+- Update cellranger to v7.1.0 ([#205](https://github.com/nf-core/scrnaseq/pull/205)).
+
+### Fixes
+
+- Autocanceling previous CI runs when new changes are pushed.
+- Fixed [#193](https://github.com/nf-core/scrnaseq/issues/177) by updating the Seurat container directive
+- Fixed [#177](https://github.com/nf-core/scrnaseq/issues/177) by adjusting the channels generation and usage when skipping fastqc
+- Fixed [#173](https://github.com/nf-core/scrnaseq/issues/173) by adjusting parameter type and adding them to modules.config
+- Fixed [#170](https://github.com/nf-core/scrnaseq/issues/170) by adding UniverSC subworkflow using new module
+- Fixed [#196](https://github.com/nf-core/scrnaseq/issues/196) by adjusting runtime requirements for AlevinQC
+- Fixed [#191](https://github.com/nf-core/scrnaseq/issues/191) by updating simpleAF containers to latest version
+
+## v2.1.0 - 2022-10-06 "Green Mercury Siberian Husky"
+
+- Alevin workflow updated to use Alevin-Fry via simpleaf - thanks to @rob-p for supporting this and @fmalmeida implementing the support
+
+### Fixes
+
+- Fixed Kallistobustools workflow [#123](https://github.com/nf-core/scrnaseq/issues/123) by upgrading to nf-core/modules module
+- Fixed matrix conversion error when running STAR with --soloFeatures GeneFull [#135](https://github.com/nf-core/scrnaseq/pull/135)
+- Fixed seurat matrix conversion error when running with conda profile [#136](https://github.com/nf-core/scrnaseq/pull/136)
+- Fixed Kallistobustools module [#116](https://github.com/nf-core/scrnaseq/issues/116). By updating nf-core module and making sure conversion modules take into account the different outputs produced by kallisto standard and non-standard workflows.
+- Updated pipeline template to [nf-core/tools 2.6](https://github.com/nf-core/tools/releases/tag/2.6)
+
+## v2.0.0 - 2022-06-17 "Gray Nickel Beagle"
+
+- Pipeline ported to dsl2
+- Template update with latest nf-core/tools v2.1
+- Added cellranger v.7.0.0 subworkflow
+- Added full size tests
+
+### Fixes
+
+- Make sure pipeline runs on multiple samples [#77](https://github.com/nf-core/scrnaseq/pull/77)
+- Fix issue where STARsolo always uses 10XV2 chemistry [#60](https://github.com/nf-core/scrnaseq/issues/60)
+
+## v1.1.0 - 2021-03-24 "Olive Mercury Corgi"
+
+- Template update with latest nf-core/tools v1.13.2
+- Parameters JSON Schema added [#42](https://github.com/nf-core/scrnaseq/issues/42)
+- [25](https://github.com/nf-core/scrnaseq/issues/25) Fix small documentation error with wrong parameter for txp2gene
+
+### Fixes
+
+- [#20](https://github.com/nf-core/scrnaseq/issues/20) Fix Transcriptome Fasta argument not detected well
+- [#21](https://github.com/nf-core/scrnaseq/issues/21) Fix `--kallisto_index` being ignored
+
+## v1.0.0 - 2019-11-28 "Tiny Aluminium Crab"
+
+Initial release of nf-core/scrnaseq, created with the [nf-core](http://nf-co.re/) template.
+This includes the following workflow options:
+
+- Salmon Alevin + AlevinQC
+- STARSolo
+- Kallisto / BUStools

CITATIONS.md

@@ -18,6 +18,21 @@
 
   > 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.
 
+* [Alevin](https://doi.org/10.1186/s13059-019-1670-y)
+
+  > Srivastava, A., Malik, L., Smith, T. et al. Alevin efficiently estimates accurate gene abundances from dscRNA-seq data. Genome Biol 20, 65 (2019).
+
+* [Salmon](https://www.nature.com/articles/nmeth.4197)
+
+  > Patro, R., Duggal, G., Love, M. et al. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 14, 417–419 (2017).
+
+* [Kallisto/Bustools](https://www.nature.com/articles/s41587-021-00870-2)
+
+  > Melsted, P., Booeshaghi, A.S., Liu, L. et al. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nat Biotechnol 39, 813–818 (2021).
+
+* [StarSolo](https://www.biorxiv.org/content/10.1101/2021.05.05.442755v1)
+  > Benjamin Kaminow, Dinar Yunusov, Alexander Dobin. STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data. BioRxiv 2021.05.05.442755 (2021).
+
 ## Software packaging/containerisation tools
 
 - [Anaconda](https://anaconda.com)