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Merge pull request #63 from nf-core/dev
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Release 1.0.0
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fbdtemme authored Oct 17, 2023
2 parents 9165416 + 3e66dda commit 1cde7e8
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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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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/pixelator then the best place to ask is on the nf-core Slack [#pixelator](https://nfcore.slack.com/channels/pixelator) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::info
If you need help using or modifying nf-core/pixelator then the best place to ask is on the nf-core Slack [#pixelator](https://nfcore.slack.com/channels/pixelator) 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)
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. 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, Charliecloud, or Apptainer)_
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14 changes: 8 additions & 6 deletions .github/workflows/awsfulltest.yml
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Expand Up @@ -14,21 +14,23 @@ jobs:
runs-on: ubuntu-latest
steps:
- name: Launch workflow via tower
uses: seqeralabs/action-tower-launch@v1
# 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
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/pixelator/work-${{ github.sha }}
parameters: |
{
"hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pixelator/results-${{ 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: seqeralabs/action-tower-launch@v1
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/pixelator/work-${{ github.sha }}
parameters: |
{
"outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/pixelator/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
5 changes: 1 addition & 4 deletions .github/workflows/ci.yml
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Expand Up @@ -24,7 +24,7 @@ jobs:
strategy:
matrix:
NXF_VER:
- "22.10.1"
- "23.04.0"
- "latest-everything"
steps:
- name: Check out pipeline code
Expand All @@ -36,8 +36,5 @@ jobs:
version: "${{ matrix.NXF_VER }}"

- 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
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
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: "3.8"
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/bluesky-post-action@v0.0.2
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 }}
#
2 changes: 2 additions & 0 deletions .gitignore
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Expand Up @@ -6,3 +6,5 @@ results/
testing/
testing*
*.pyc
.idea
.vscode
5 changes: 5 additions & 0 deletions .gitpod.yml
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@@ -1,4 +1,9 @@
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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8 changes: 8 additions & 0 deletions .nf-core.yml
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@@ -1 +1,9 @@
repository_type: pipeline
lint:
# No multiqc support for now
multiqc_config: false
files_exist:
- assets/multiqc_config.yml
- conf/igenomes.config
files_unchanged:
- lib/NfcoreTemplate.groovy
19 changes: 18 additions & 1 deletion .pre-commit-config.yaml
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@@ -1,5 +1,22 @@
repos:
- repo: https://github.com/pre-commit/mirrors-prettier
rev: "v2.7.1"
rev: "v3.0.0-alpha.9-for-vscode"
hooks:
- id: prettier

- repo: https://github.com/psf/black
rev: 23.3.0
hooks:
- id: black

- repo: local
hooks:
- id: nf-core/tools parameters.yaml
name: Update nf-params.yml file with schema
language: python
additional_dependencies:
- nf-core
entry: nf-core
args: [create-params-file, --output, assets/nf-params.yml, "--force", "."]
pass_filenames: false
files: ^nextflow_schema.json$
1 change: 1 addition & 0 deletions .prettierignore
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Expand Up @@ -10,3 +10,4 @@ testing/
testing*
*.pyc
bin/
assets/nf-params.yml
12 changes: 2 additions & 10 deletions CHANGELOG.md
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Expand Up @@ -3,14 +3,6 @@
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).

## v1.0.0dev - [date]
## 1.0.0 - [2023-10-17]

Initial release of nf-core/pixelator, created with the [nf-core](https://nf-co.re/) template.

### `Added`

### `Fixed`

### `Dependencies`

### `Deprecated`
Initial release of nf-core/pixelator.
16 changes: 13 additions & 3 deletions CITATIONS.md
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Expand Up @@ -10,10 +10,17 @@
## Pipeline tools

- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
- [pixelator](https://doi.org/10.1101/2023.06.05.543770)

- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
> 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.
> Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770.
- [cutadapt](http://dx.doi.org/10.14806/ej.17.1.200)

> Martin, Marcel. “Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads.” EMBnet.Journal 17, no. 1 (May 2, 2011): 10–12. https://doi.org/10.14806/ej.17.1.200.
- [fastp](https://doi.org/10.1002/imt2.107)

> Chen, Shifu. “Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” IMeta 2, no. 2 (2023): e107. https://doi.org/10.1002/imt2.107.
## Software packaging/containerisation tools

Expand All @@ -31,5 +38,8 @@
- [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)

> Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
- [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)

> Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.
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