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Merge pull request #178 from nf-core/dev
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Dev -> master for v1.3.0
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pinin4fjords authored Oct 24, 2023
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1 change: 1 addition & 0 deletions .devcontainer/devcontainer.json
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"name": "nfcore",
"image": "nfcore/gitpod:latest",
"remoteUser": "gitpod",
"runArgs": ["--privileged"],

// Configure tool-specific properties.
"customizations": {
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2 changes: 1 addition & 1 deletion .editorconfig
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Expand Up @@ -8,7 +8,7 @@ trim_trailing_whitespace = true
indent_size = 4
indent_style = space

[*.{md,yml,yaml,html,css,scss,js,cff}]
[*.{md,yml,yaml,html,css,scss,js}]
indent_size = 2

# These files are edited and tested upstream in nf-core/modules
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5 changes: 3 additions & 2 deletions .github/CONTRIBUTING.md
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Expand Up @@ -9,7 +9,9 @@ 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 ;)

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

## Contribution workflow

Expand Down Expand Up @@ -116,4 +118,3 @@ To get started:
Devcontainer specs:

- [DevContainer config](.devcontainer/devcontainer.json)
- [Dockerfile](.devcontainer/Dockerfile)
4 changes: 2 additions & 2 deletions .github/ISSUE_TEMPLATE/bug_report.yml
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Expand Up @@ -42,9 +42,9 @@ body:
attributes:
label: System information
description: |
* Nextflow version _(eg. 22.10.1)_
* Nextflow version _(eg. 23.04.0)_
* Hardware _(eg. HPC, Desktop, Cloud)_
* Executor _(eg. slurm, local, awsbatch)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
* Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
* OS _(eg. CentOS Linux, macOS, Linux Mint)_
* Version of nf-core/differentialabundance _(eg. 1.1, 1.5, 1.8.2)_
3 changes: 2 additions & 1 deletion .github/PULL_REQUEST_TEMPLATE.md
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Expand Up @@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/diff

- [ ] 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/differentialabundance/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/differentialabundance _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/differentialabundance/tree/master/.github/CONTRIBUTING.md)
- [ ] If necessary, also make a PR on the nf-core/differentialabundance _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>`).
- [ ] Usage Documentation in `docs/usage.md` is updated.
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11 changes: 8 additions & 3 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -14,18 +14,23 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: nf-core/tower-action@v3
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/differentialabundance/work-${{ github.sha }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/differentialabundance/results-${{ github.sha }}"
}
profiles: test_full,aws_tower
profiles: test_full

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json
10 changes: 7 additions & 3 deletions .github/workflows/awstest.yml
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Expand Up @@ -12,18 +12,22 @@ jobs:
steps:
# Launch workflow using Tower CLI tool action
- name: Launch workflow via tower
uses: nf-core/tower-action@v3
uses: seqeralabs/action-tower-launch@v2
with:
workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
revision: ${{ github.sha }}
workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/differentialabundance/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/differentialabundance/results-test-${{ github.sha }}"
}
profiles: test,aws_tower
profiles: test

- uses: actions/upload-artifact@v3
with:
name: Tower debug log file
path: tower_action_*.log
path: |
tower_action_*.log
tower_action_*.json
2 changes: 1 addition & 1 deletion .github/workflows/branch.yml
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Expand Up @@ -13,7 +13,7 @@ jobs:
- name: Check PRs
if: github.repository == 'nf-core/differentialabundance'
run: |
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/differentialabundance ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
{ [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/differentialabundance ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
# If the above check failed, post a comment on the PR explaining the failure
# NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
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4 changes: 3 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -24,12 +24,14 @@ jobs:
strategy:
matrix:
NXF_VER:
- "22.10.1"
- "23.04.0"
- "latest-everything"
profile:
- "test"
- "test_nogtf"
- "test_affy"
- "test_maxquant"
- "test_soft"
steps:
- name: Check out pipeline code
uses: actions/checkout@v3
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24 changes: 24 additions & 0 deletions .github/workflows/clean-up.yml
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name: "Close user-tagged issues and PRs"
on:
schedule:
- cron: "0 0 * * 0" # Once a week

jobs:
clean-up:
runs-on: ubuntu-latest
permissions:
issues: write
pull-requests: write
steps:
- uses: actions/stale@v7
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."
close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
days-before-stale: 30
days-before-close: 20
days-before-pr-close: -1
any-of-labels: "awaiting-changes,awaiting-feedback"
exempt-issue-labels: "WIP"
exempt-pr-labels: "WIP"
repo-token: "${{ secrets.GITHUB_TOKEN }}"
2 changes: 1 addition & 1 deletion .github/workflows/linting.yml
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Expand Up @@ -78,7 +78,7 @@ jobs:

- uses: actions/setup-python@v4
with:
python-version: "3.7"
python-version: "3.11"
architecture: "x64"

- name: Install dependencies
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68 changes: 68 additions & 0 deletions .github/workflows/release-announcments.yml
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name: release-announcements
# Automatic release toot and tweet anouncements
on:
release:
types: [published]
workflow_dispatch:

jobs:
toot:
runs-on: ubuntu-latest
steps:
- uses: rzr/fediverse-action@master
with:
access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
host: "mstdn.science" # custom host if not "mastodon.social" (default)
# GitHub event payload
# https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
message: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Please see the changelog: ${{ github.event.release.html_url }}
send-tweet:
runs-on: ubuntu-latest

steps:
- uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install dependencies
run: pip install tweepy==4.14.0
- name: Send tweet
shell: python
run: |
import os
import tweepy
client = tweepy.Client(
access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
)
tweet = os.getenv("TWEET")
client.create_tweet(text=tweet)
env:
TWEET: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Please see the changelog: ${{ github.event.release.html_url }}
TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}

bsky-post:
runs-on: ubuntu-latest
steps:
- uses: zentered/[email protected]
with:
post: |
Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
Please see the changelog: ${{ github.event.release.html_url }}
env:
BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
#
5 changes: 5 additions & 0 deletions .gitpod.yml
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image: nfcore/gitpod:latest
tasks:
- name: Update Nextflow and setup pre-commit
command: |
pre-commit install --install-hooks
nextflow self-update
vscode:
extensions: # based on nf-core.nf-core-extensionpack
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5 changes: 5 additions & 0 deletions .pre-commit-config.yaml
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@@ -0,0 +1,5 @@
repos:
- repo: https://github.com/pre-commit/mirrors-prettier
rev: "v2.7.1"
hooks:
- id: prettier
38 changes: 38 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -3,6 +3,43 @@
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).

## v1.3.0 - 2023-10-25

### `Added`

- [[#124](https://github.com/nf-core/differentialabundance/pull/124)] - Template update for nf-core/tools v2.8 ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jasmezz](https://github.com/jasmezz))
- [[#129](https://github.com/nf-core/differentialabundance/pull/129)] - Module updates to fit with recent registry changes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@maxulysse](https://github.com/maxulysse), [@adamrtalbot](https://github.com/adamrtalbot))
- [[#130](https://github.com/nf-core/differentialabundance/pull/130)] - Document reasons for lack of differential expression ([@pinin4fjords](https://github.com/pinin4fjords), review by [@jfy133](https://github.com/jfy133))
- [[#131](https://github.com/nf-core/differentialabundance/pull/131)] - Improve gtf to table configurability ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
- [# 136](https://github.com/nf-core/differentialabundance/pull/136)] - Added support for non-Affymetrix arrays via automatic download of SOFT matrices in GEO ([@azedinez](https://github.com/azedinez), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#137](https://github.com/nf-core/differentialabundance/pull/137)] - Add `--sizefactors_from_controls` and `--gene_id_col` for DESeq2 module to modules.config ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#145](https://github.com/nf-core/differentialabundance/pull/145)] - Template update for nf-core/tools v2.9 ([@nf-core-bot](https://github.com/nf-core-bot), review by [@pinin4fjords](https://github.com/pinin4fjords), [@WackerO](https://github.com/WackerO))
- [[#147](https://github.com/nf-core/differentialabundance/pull/147)] - Add Maxquant analysis module ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#166](https://github.com/nf-core/differentialabundance/issues/166)] - Output a parameter-resolved R Markdown document, as well as rendered HTML ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
- [[#119](https://github.com/nf-core/differentialabundance/issues/119)] - Document sample sheet for Affy arrays ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
- [[#165](https://github.com/nf-core/differentialabundance/issues/165)] - Update subway map ([@pinin4fjords](https://github.com/pinin4fjords), review by [@FriederikeHanssen](https://github.com/FriederikeHanssen))
- [[#135](https://github.com/nf-core/differentialabundance/issues/135)] - workaround OPENBLAS using all cores problem ([@pinin4fjords](https://github.com/pinin4fjords), review by [@sateeshperi](https://github.com/sateeshperi))
- [[#176](https://github.com/nf-core/differentialabundance/pull/176)] - bump shinyngs ([@pinin4fjords](https://github.com/pinin4fjords), review by )

### `Fixed`

- [[#116](https://github.com/nf-core/differentialabundance/issues/116)] - Skip outlier detection with low replication ([@pinin4fjords](https://github.com/pinin4fjords), review by [@nvnieuwk](https://github.com/nvnieuwk))
- [[#122](https://github.com/nf-core/differentialabundance/pull/126)] - Add spaces to satisfy nf-core download for singularity ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
- [[#127](https://github.com/nf-core/differentialabundance/issues/127)] - [Bug] Can't pass samplesheet with -c file.config , or -params-file params.yml or directly with --input samplesheet.csv ([@ctuni](https://github.com/ctuni), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#138](https://github.com/nf-core/differentialabundance/issues/138)]- Fix bugs with --control_features and --sizefactors_from_controls ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#133](https://github.com/nf-core/differentialabundance/issues/133)] - Sample exclusion options fail due to contrast-wise normalisation ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
- [[#160](https://github.com/nf-core/differentialabundance/issues/160)]- Fix merge conflicts for Template update 2.10 by nf-core-bot ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#164](https://github.com/nf-core/differentialabundance/pull/164)] - Rlog + other small fixes ([@pinin4fjords](https://github.com/pinin4fjords), review by [@drpatelh](https://github.com/drpatelh))
- [[#174](https://github.com/nf-core/differentialabundance/pull/174)] - Fix metro map ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))

### `Changed`

- [[#179](https://github.com/nf-core/differentialabundance/issues/179)] - Removed shiny app error message for proteus runs ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#159](https://github.com/nf-core/differentialabundance/issues/159)] - CUSTOM/MATRIXFILTER module update ([@WackerO](https://github.com/WackerO), review by [@suzannejin](https://github.com/suzannejin))
- [[#154](https://github.com/nf-core/differentialabundance/issues/154)] - RMARKDOWNNOTEBOOK env update ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#151](https://github.com/nf-core/differentialabundance/issues/151)] - Module update ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#147](https://github.com/nf-core/differentialabundance/pull/147)] - RMARKDOWNNOTEBOOK env update, SHINYNGS and CUSTOM update ([@WackerO](https://github.com/WackerO), review by [@pinin4fjords](https://github.com/pinin4fjords))

## v1.2.0 - 2023-04-19

### `Added`
Expand All @@ -11,6 +48,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#105](https://github.com/nf-core/differentialabundance/pull/105)] - Enabled multiple GMT/GMX files for GSEA ([@WackerO](https://github.com/WackerO), reported by [@grst](https://github.com/grst), review by [@pinin4fjords](https://github.com/pinin4fjords))
- [[#108](https://github.com/nf-core/differentialabundance/issues/108)] - Add shiny app generation (starting feature set) ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO))
- [[#110](https://github.com/nf-core/differentialabundance/pull/110)] - Add shiny app outputs to tower.yml ([@pinin4fjords](https://github.com/pinin4fjords), review by [@WackerO](https://github.com/WackerO), [@maxulysse](https://github.com/maxulysse))
- [[#149]](https://github.com/nf-core/differentialabundance/pull/149) - Update README.md - add ref to nf-core/rnaseq and Affymetrix ([@smoe](https://github.com/smoe), review by [@pinin4fjords](https://github.com/pinin4fjords))

### `Fixed`

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