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10 changes: 1 addition & 9 deletions .devcontainer/devcontainer.json
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Expand Up @@ -10,15 +10,7 @@
"vscode": {
// Set *default* container specific settings.json values on container create.
"settings": {
"python.defaultInterpreterPath": "/opt/conda/bin/python",
"python.linting.enabled": true,
"python.linting.pylintEnabled": true,
"python.formatting.autopep8Path": "/opt/conda/bin/autopep8",
"python.formatting.yapfPath": "/opt/conda/bin/yapf",
"python.linting.flake8Path": "/opt/conda/bin/flake8",
"python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
"python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
"python.linting.pylintPath": "/opt/conda/bin/pylint"
"python.defaultInterpreterPath": "/opt/conda/bin/python"
},

// Add the IDs of extensions you want installed when the container is created.
Expand Down
9 changes: 7 additions & 2 deletions .editorconfig
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Expand Up @@ -18,7 +18,12 @@ end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset
indent_size = unset
[/subworkflows/nf-core/**]
charset = unset
end_of_line = unset
insert_final_newline = unset
trim_trailing_whitespace = unset
indent_style = unset

[/assets/email*]
indent_size = unset
Expand All @@ -28,5 +33,5 @@ indent_size = unset
indent_style = unset

# ignore python
[*.{py}]
[*.{py,md}]
indent_style = unset
14 changes: 8 additions & 6 deletions .github/CONTRIBUTING.md
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Expand Up @@ -9,9 +9,8 @@ Please use the pre-filled template to save time.
However, don't be put off by this template - other more general issues and suggestions are welcome!
Contributions to the code are even more welcome ;)

:::info
If you need help using or modifying nf-core/scrnaseq then the best place to ask is on the nf-core Slack [#scrnaseq](https://nfcore.slack.com/channels/scrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::
> [!NOTE]
> If you need help using or modifying nf-core/scrnaseq then the best place to ask is on the nf-core Slack [#scrnaseq](https://nfcore.slack.com/channels/scrnaseq) channel ([join our Slack here](https://nf-co.re/join/slack)).
## Contribution workflow

Expand All @@ -27,8 +26,11 @@ If you're not used to this workflow with git, you can start with some [docs from

## Tests

You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
You have the option to test your changes locally by running the pipeline. For receiving warnings about process selectors and other `debug` information, it is recommended to use the debug profile. Execute all the tests with the following command:

```bash
nf-test test --profile debug,test,docker --verbose
```

When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
Expand Down Expand Up @@ -90,7 +92,7 @@ Once there, use `nf-core schema build` to add to `nextflow_schema.json`.

Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels.

The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block.
The process resources can be passed on to the tool dynamically within the process with the `${task.cpus}` and `${task.memory}` variables in the `script:` block.

### Naming schemes

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2 changes: 1 addition & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -18,7 +18,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/scrn
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/scrnaseq/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/scrnaseq _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 (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
- [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`).
- [ ] 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.
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/branch.yml
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Expand Up @@ -19,7 +19,7 @@ jobs:
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
- name: Post PR comment
if: failure()
uses: mshick/add-pr-comment@v2
uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
with:
message: |
## This PR is against the `master` branch :x:
Expand Down
10 changes: 3 additions & 7 deletions .github/workflows/ci.yml
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Expand Up @@ -36,15 +36,11 @@ jobs:
profile: ["alevin", "cellranger", "kallisto", "star"]

steps:
- name: Free some space
run: |
sudo rm -rf /usr/share/dotnet
sudo rm -rf /opt/ghc
sudo rm -rf "/usr/local/share/boost"
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
- name: Disk space cleanup
uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1

- name: Check out pipeline code
uses: actions/checkout@v4
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
Expand Down
2 changes: 1 addition & 1 deletion .github/workflows/clean-up.yml
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Expand Up @@ -10,7 +10,7 @@ jobs:
issues: write
pull-requests: write
steps:
- uses: actions/stale@v9
- uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
with:
stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
Expand Down
13 changes: 9 additions & 4 deletions .github/workflows/download_pipeline.yml
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Expand Up @@ -6,6 +6,11 @@ name: Test successful pipeline download with 'nf-core download'
# - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
on:
workflow_dispatch:
inputs:
testbranch:
description: "The specific branch you wish to utilize for the test execution of nf-core download."
required: true
default: "dev"
pull_request:
types:
- opened
Expand All @@ -25,11 +30,11 @@ jobs:
- name: Install Nextflow
uses: nf-core/setup-nextflow@v1

- uses: actions/setup-python@v5
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
python-version: "3.11"
architecture: "x64"
- uses: eWaterCycle/setup-singularity@v7
- uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
with:
singularity-version: 3.8.3

Expand All @@ -42,13 +47,13 @@ jobs:
run: |
echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
- name: Download the pipeline
env:
NXF_SINGULARITY_CACHEDIR: ./
run: |
nf-core download ${{ env.REPO_LOWERCASE }} \
nf-core download ${{ env.REPO_LOWERCASE }} \
--revision ${{ env.REPO_BRANCH }} \
--outdir ./${{ env.REPOTITLE_LOWERCASE }} \
--compress "none" \
Expand Down
10 changes: 5 additions & 5 deletions .github/workflows/linting.yml
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Expand Up @@ -14,10 +14,10 @@ jobs:
pre-commit:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

- name: Set up Python 3.11
uses: actions/setup-python@v5
uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
python-version: 3.11
cache: "pip"
Expand All @@ -32,12 +32,12 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v4
uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1

- uses: actions/setup-python@v5
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
python-version: "3.11"
architecture: "x64"
Expand All @@ -60,7 +60,7 @@ jobs:

- name: Upload linting log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@v4
uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
with:
name: linting-logs
path: |
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/linting_comment.yml
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Expand Up @@ -11,7 +11,7 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Download lint results
uses: dawidd6/action-download-artifact@v3
uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
with:
workflow: linting.yml
workflow_conclusion: completed
Expand All @@ -21,7 +21,7 @@ jobs:
run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT

- name: Post PR comment
uses: marocchino/sticky-pull-request-comment@v2
uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
with:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
number: ${{ steps.pr_number.outputs.pr_number }}
Expand Down
11 changes: 9 additions & 2 deletions .github/workflows/release-announcements.yml
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Expand Up @@ -9,6 +9,11 @@ jobs:
toot:
runs-on: ubuntu-latest
steps:
- name: get topics and convert to hashtags
id: get_topics
run: |
curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
- uses: rzr/fediverse-action@master
with:
access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
Expand All @@ -20,11 +25,13 @@ jobs:
Please see the changelog: ${{ github.event.release.html_url }}
${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
send-tweet:
runs-on: ubuntu-latest

steps:
- uses: actions/setup-python@v5
- uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
with:
python-version: "3.10"
- name: Install dependencies
Expand Down Expand Up @@ -56,7 +63,7 @@ jobs:
bsky-post:
runs-on: ubuntu-latest
steps:
- uses: zentered/[email protected]
- uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
with:
post: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Expand Down
3 changes: 2 additions & 1 deletion .gitignore
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Expand Up @@ -9,4 +9,5 @@ testing*
log/
reports/
testme.sh
.nf-test/
.nf-test*
.vscode
6 changes: 2 additions & 4 deletions .gitpod.yml
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Expand Up @@ -10,13 +10,11 @@ tasks:
vscode:
extensions: # based on nf-core.nf-core-extensionpack
- codezombiech.gitignore # Language support for .gitignore files
# - cssho.vscode-svgviewer # SVG viewer
- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed
- EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- mechatroner.rainbow-csv # Highlight columns in csv files in different colors
# - nextflow.nextflow # Nextflow syntax highlighting
# - nextflow.nextflow # Nextflow syntax highlighting
- oderwat.indent-rainbow # Highlight indentation level
- streetsidesoftware.code-spell-checker # Spelling checker for source code
- charliermarsh.ruff # Code linter Ruff
5 changes: 5 additions & 0 deletions .nf-core.yml
Original file line number Diff line number Diff line change
Expand Up @@ -3,3 +3,8 @@ 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
4 changes: 3 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -5,7 +5,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

## v2.6.0dev - [date]

- [[#91](https://github.com/nf-core/scrnaseq/issues/91)] - Change from pytests to nf-test
- 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))

## v2.5.1

Expand Down
12 changes: 8 additions & 4 deletions README.md
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Expand Up @@ -4,14 +4,18 @@
<img alt="nf-core/scrnaseq" src="docs/images/nf-core-scrnaseq_logo_light.png">
</picture>
</h1>

[![GitHub Actions CI Status](https://github.com/nf-core/scrnaseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/scrnaseq/actions?query=workflow%3A%22nf-core+CI%22)
[![GitHub Actions Linting Status](https://github.com/nf-core/scrnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/scrnaseq/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/scrnaseq/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3568187-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3568187)
[![GitHub Actions Linting Status](https://github.com/nf-core/scrnaseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/scrnaseq/actions?query=workflow%3A%22nf-core+linting%22)
[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/scrnaseq/results)
[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3568187-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3568187)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
[![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 Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/scrnaseq)
[![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/scrnaseq)

[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23scrnaseq-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/scrnaseq)[![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)

Expand Down Expand Up @@ -44,8 +48,8 @@ First, prepare a samplesheet with your input data that looks as follows:

```csv
sample,fastq_1,fastq_2,expected_cells
pbmc8k,pbmc8k_S1_L007_R1_001.fastq.gz,pbmc8k_S1_L007_R2_001.fastq.gz,"10000"
pbmc8k,pbmc8k_S1_L008_R1_001.fastq.gz,pbmc8k_S1_L008_R2_001.fastq.gz,"10000"
pbmc8k,pbmc8k_S1_L007_R1_001.fastq.gz,pbmc8k_S1_L007_R2_001.fastq.gz,10000
pbmc8k,pbmc8k_S1_L008_R1_001.fastq.gz,pbmc8k_S1_L008_R2_001.fastq.gz,10000
```

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
Expand Down
2 changes: 2 additions & 0 deletions assets/multiqc_config.yml
Original file line number Diff line number Diff line change
Expand Up @@ -11,3 +11,5 @@ report_section_order:
order: -1002

export_plots: true

disable_version_detection: true
37 changes: 24 additions & 13 deletions assets/schema_input.json
Original file line number Diff line number Diff line change
Expand Up @@ -10,27 +10,38 @@
"sample": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Sample name must be provided and cannot contain spaces"
"errorMessage": "Sample name must be provided and cannot contain spaces",
"meta": ["id"]
},
"fastq_1": {
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
},
"fastq_2": {
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+\\.f(ast)?q\\.gz$"
},
{
"type": "string",
"maxLength": 0
}
]
"type": "string",
"format": "file-path",
"exists": true,
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
},
"expected_cells": {
"type": "integer",
"errorMessage": "Expected cells must be an Integer",
"meta": ["expected_cells"]
},
"seq_center": {
"type": "string",
"meta": ["seq_center"]
},
"sample_type": {
"type": "string",
"enum": ["atac", "gex"],
"meta": ["sample_type"]
}
},
"required": ["sample", "fastq_1"]
"required": ["sample", "fastq_1", "fastq_2"]
}
}
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