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Merge pull request #104 from nf-core/dev
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Dev -> Master for 2.1.0 release
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edmundmiller authored Feb 15, 2023
2 parents 985f37e + 91ecf55 commit 12e9ba6
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27 changes: 27 additions & 0 deletions .devcontainer/devcontainer.json
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{
"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",

// Configure tool-specific properties.
"customizations": {
// Configure properties specific to VS Code.
"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"
},

// Add the IDs of extensions you want installed when the container is created.
"extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
}
}
}
1 change: 1 addition & 0 deletions .gitattributes
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@@ -1,3 +1,4 @@
*.config linguist-language=nextflow
*.nf.test linguist-language=nextflow
modules/nf-core/** linguist-generated
subworkflows/nf-core/** linguist-generated
16 changes: 16 additions & 0 deletions .github/CONTRIBUTING.md
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Expand Up @@ -101,3 +101,19 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
### Images and figures

For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).

## GitHub Codespaces

This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.

To get started:

- Open the repo in [Codespaces](https://github.com/nf-core/nascent/codespaces)
- Tools installed
- nf-core
- Nextflow

Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
- [Dockerfile](.devcontainer/Dockerfile)
2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -42,7 +42,7 @@ body:
attributes:
label: System information
description: |
* Nextflow version _(eg. 21.10.3)_
* Nextflow version _(eg. 22.10.1)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
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60 changes: 51 additions & 9 deletions .github/workflows/ci.yml
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Expand Up @@ -11,30 +11,72 @@ on:
env:
NXF_ANSI_LOG: false

concurrency:
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
cancel-in-progress: true

jobs:
test:
name: Run pipeline with test data
name: nf-test ${{ matrix.profile }}-${{ matrix.NXF_VER }}
# Only run on push if this is the nf-core dev branch (merged PRs)
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/nascent') }}"
runs-on: ubuntu-latest
strategy:
matrix:
NXF_VER:
- "21.10.6"
- "22.10.1"
- "latest-everything"
parameters:
- ""
- "--aligner bwamem2"
- "--aligner dragmap"
profile: ["docker"] # TODO , "singularity", "conda"]
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
uses: actions/checkout@v3

- name: Cache Nextflow installation
id: cache-software
uses: actions/cache@v3
with:
path: |
/usr/local/bin/nf-test
/home/runner/.nf-test/nf-test.jar
key: nascent-${{ runner.os }}-${{ matrix.NXF_VER }}

- name: Install Nextflow
uses: nf-core/setup-nextflow@v1
with:
version: "${{ matrix.NXF_VER }}"

- name: Run pipeline with test data
- 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: Set up Singularity
if: matrix.profile == 'singularity'
uses: eWaterCycle/setup-singularity@v5
with:
singularity-version: 3.7.1

- name: Set up miniconda
if: matrix.profile == 'conda'
uses: conda-incubator/setup-miniconda@v2
with:
auto-update-conda: true
channels: conda-forge,bioconda,defaults
python-version: ${{ matrix.python-version }}

- name: Conda clean
if: matrix.profile == 'conda'
run: conda clean -a

- name: Run nf-test
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker ${{ matrix.parameters }} --outdir ./results
nf-test test \
--profile=${{ matrix.profile }} \
tests/pipeline/*.nf.test \
--tap=test.tap
- uses: pcolby/tap-summary@v1
with:
path: >-
test.tap
6 changes: 3 additions & 3 deletions .github/workflows/fix-linting.yml
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Expand Up @@ -24,7 +24,7 @@ jobs:
env:
GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}

- uses: actions/setup-node@v2
- uses: actions/setup-node@v3

- name: Install Prettier
run: npm install -g prettier @prettier/plugin-php
Expand All @@ -34,9 +34,9 @@ jobs:
id: prettier_status
run: |
if prettier --check ${GITHUB_WORKSPACE}; then
echo "::set-output name=result::pass"
echo "result=pass" >> $GITHUB_OUTPUT
else
echo "::set-output name=result::fail"
echo "result=fail" >> $GITHUB_OUTPUT
fi
- name: Run 'prettier --write'
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18 changes: 10 additions & 8 deletions .github/workflows/linting.yml
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Expand Up @@ -4,6 +4,8 @@ name: nf-core linting
# that the code meets the nf-core guidelines.
on:
push:
branches:
- dev
pull_request:
release:
types: [published]
Expand All @@ -12,9 +14,9 @@ jobs:
EditorConfig:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: actions/setup-node@v2
- uses: actions/setup-node@v3

- name: Install editorconfig-checker
run: npm install -g editorconfig-checker
Expand All @@ -25,9 +27,9 @@ jobs:
Prettier:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- uses: actions/setup-node@v2
- uses: actions/setup-node@v3

- name: Install Prettier
run: npm install -g prettier
Expand All @@ -38,7 +40,7 @@ jobs:
PythonBlack:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3

- name: Check code lints with Black
uses: psf/black@stable
Expand Down Expand Up @@ -69,12 +71,12 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Check out pipeline code
uses: actions/checkout@v2
uses: actions/checkout@v3

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

- uses: actions/setup-python@v3
- uses: actions/setup-python@v4
with:
python-version: "3.7"
architecture: "x64"
Expand All @@ -97,7 +99,7 @@ jobs:

- name: Upload linting log file artifact
if: ${{ always() }}
uses: actions/upload-artifact@v2
uses: actions/upload-artifact@v3
with:
name: linting-logs
path: |
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2 changes: 1 addition & 1 deletion .github/workflows/linting_comment.yml
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Expand Up @@ -18,7 +18,7 @@ jobs:

- name: Get PR number
id: pr_number
run: echo "::set-output name=pr_number::$(cat linting-logs/PR_number.txt)"
run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT

- name: Post PR comment
uses: marocchino/sticky-pull-request-comment@v2
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1 change: 1 addition & 0 deletions .gitignore
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Expand Up @@ -6,3 +6,4 @@ results/
testing/
testing*
*.pyc
.nf-test
2 changes: 2 additions & 0 deletions .prettierignore
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@@ -1,5 +1,6 @@
email_template.html
adaptivecard.json
slackreport.json
.nextflow*
work/
data/
Expand All @@ -8,3 +9,4 @@ results/
testing/
testing*
*.pyc
bin/
25 changes: 21 additions & 4 deletions CHANGELOG.md
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Expand Up @@ -3,9 +3,26 @@
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).

## v2.0.0 - 2022-10-20
## v2.1.0 - 2023-02-15

### `Added`
### Added

- [[#94](https://github.com/nf-core/nascent/pull/94)] - Added a second BEDTools intersect step to allow filtering and overlapping in the same workflow.
- [[#101](https://github.com/nf-core/nascent/pull/101)] - Initialized nf-test

### Changed

- [[#103](https://github.com/nf-core/nascent/pull/103)] - Updated Modules

### Fixed

- [[841ae62](https://github.com/nf-core/nascent/commit/841ae62)] - Updated PINTS version from 1.1.6 to 1.1.8 ([Fixes an issue where PINTS fails if one of the predictions was empty](https://github.com/hyulab/PINTS/issues/12))
- [[#97](https://github.com/nf-core/nascent/pull/97)] - Add HOMER channels to fix error about "Missing workflow output parameter: homer_peaks" when homer is skipped
- Add missing DOIs (@apeltzer)

## v2.0.0 - 2022-10-24

### Added

- DSL2 conversion
- [[#28](https://github.com/nf-core/nascent/issues/28)] - Added DRAGMAP alignment
Expand All @@ -14,11 +31,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#71](https://github.com/nf-core/nascent/issues/71)] - Add FASTP for adapter trimming
- [[#77](https://github.com/nf-core/nascent/issues/77)] - Add dedup subworkflow

### `Fixed`
### Fixed

- [[#33](https://github.com/nf-core/nascent/issues/33)] - groHMM works on full runs. Added the keep standard chromosomes function to standardize bam files.

### `Dependencies`
### Dependencies

- Updated Nextflow version to `v21.10.6`

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56 changes: 0 additions & 56 deletions CITATION.cff

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6 changes: 6 additions & 0 deletions CITATIONS.md
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Expand Up @@ -72,6 +72,12 @@

> Smith T, Heger A, Sudbery I. UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy Genome Res. 2017 Mar;27(3):491-499. doi: 10.1101/gr.209601.116. Epub 2017 Jan 18. PubMed PMID: 28100584; PubMed Central PMCID: PMC5340976.
## Python packages

- [Pandas](https://pandas.pydata.org/about/citing.html)

> The pandas development team. (2022). pandas-dev/pandas: Pandas (v1.5.2). Zenodo. doi: 10.5281/zenodo.3509134
## R packages

- [R](https://www.R-project.org/)
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