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Merge pull request #117 from JoseEspinosa/merge_temp_2.10
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Merge template v2.10
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JoseEspinosa authored Sep 27, 2023
2 parents bbc2265 + aae18b5 commit e9fad86
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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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4 changes: 3 additions & 1 deletion .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/proteinfold then the best place to ask is on the nf-core Slack [#proteinfold](https://nfcore.slack.com/channels/proteinfold) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::info
If you need help using or modifying nf-core/proteinfold then the best place to ask is on the nf-core Slack [#proteinfold](https://nfcore.slack.com/channels/proteinfold) channel ([join our Slack here](https://nf-co.re/join/slack)).
:::

## Contribution workflow

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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/[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 }}
#
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [PR #112](https://github.com/nf-core/rnaseq/pull/112) - Use `nf-validation` plugin for parameter and samplesheet validation.
- [#113](https://github.com/nf-core/proteinfold/pull/113) - Include esmfold dbs for full data sets.
- [PR #114](https://github.com/nf-core/rnaseq/pull/114) - Update paths to test dbs.
- [PR #117](https://github.com/nf-core/proteinfold/pull/117) - Update pipeline template to [nf-core/tools 2.10](https://github.com/nf-core/tools/releases/tag/2.10).

## 1.0.0 - White Silver Reebok

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2 changes: 1 addition & 1 deletion CITATIONS.md
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- [ESMFold](https://pubmed.ncbi.nlm.nih.gov/36927031/)
Lin Z, Akin H, Rao R, Hie B, Zhu Z, Lu W, Smetanin N, Verkuil R, Kabeli O, Shmueli Y, Dos Santos Costa A, Fazel-Zarandi M, Sercu T, Candido S, Rives A. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science. 2023 Mar 17;379(6637):1123-1130. doi: 10.1126/science.ade2574. Epub 2023 Mar 16. PMID: 36927031.

> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
> Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)

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