Merge pull request #213 from christopher-mohr/update_pipeline_and_fix…

…_biomart_con

Update epytope and Ensembl reference handling

.devcontainer/devcontainer.json

@@ -2,6 +2,7 @@
  "name": "nfcore",
  "image": "nfcore/gitpod:latest",
  "remoteUser": "gitpod",
+ "runArgs": ["--privileged"],
 
  // Configure tool-specific properties.
  "customizations": {

.github/CONTRIBUTING.md

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

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
  - uses: actions/setup-python@v4
  with:
- python-version: "3.8"
+ python-version: "3.11"
  architecture: "x64"
 
  - name: Install dependencies

.github/workflows/release-announcments.yml

@@ -0,0 +1,68 @@
+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 }}
+ #

CHANGELOG.md

@@ -3,10 +3,12 @@
 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).
 
-## v2.2.2dev - 2023-08-29
+## v2.3dev - 2023-08-29
 
 ### `Changed`
 
+- [213](https://github.com/nf-core/epitopeprediction/pull/203) - Rename param `genome_version` to `genome_reference`, add functionality to handle BioMart archive urls
+- [213](https://github.com/nf-core/epitopeprediction/pull/203) - Update to nf-core template `2.10`
 - [203](https://github.com/nf-core/epitopeprediction/pull/203) - Update to nf-core template `2.9`
 - [203](https://github.com/nf-core/epitopeprediction/pull/203) - Update to nf-core template `2.8`
 - [#206](https://github.com/nf-core/epitopeprediction/issues/206) - Update the row checker class.

README.md

@@ -1,9 +1,7 @@
 # ![nf-core/epitopeprediction](docs/images/nf-core-epitopeprediction_logo_light.png#gh-light-mode-only) ![nf-core/epitopeprediction](docs/images/nf-core-epitopeprediction_logo_dark.png#gh-dark-mode-only)
 
 [![GitHub Actions CI Status](https://github.com/nf-core/epitopeprediction/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/epitopeprediction/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/epitopeprediction/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/epitopeprediction/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/epitopeprediction/results)
-[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3564666-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3564666)
+[![GitHub Actions Linting Status](https://github.com/nf-core/epitopeprediction/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/epitopeprediction/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/epitopeprediction/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3564666-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3564666)
 
 [![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/)
@@ -30,7 +28,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 ## Usage
 
-> **Note**
+> [!NOTE]
 > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
 > to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
 > with `-profile test` before running the workflow on actual data.
@@ -55,8 +53,8 @@ nextflow run nf-core/epitopeprediction \
  --outdir <OUTDIR>
 ````
 
-> **Warning:**
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
+> [!WARNING]
+> Please provide pipeline parameters via the CLI or Nextflow > > `-params-file` option. Custom config files including those
 > provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
 > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
 

assets/multiqc_config.yml

@@ -1,12 +1,7 @@
 report_comment: >
- This report has been generated by the <a href="https://github.com/nf-core/epitopeprediction/2.2.2dev" target="_blank">nf-core/epitopeprediction</a>
+ This report has been generated by the <a href="https://github.com/nf-core/epitopeprediction/releases/tag/dev" target="_blank">nf-core/epitopeprediction</a>
  analysis pipeline. For information about how to interpret these results, please see the
- <a href="https://nf-co.re/epitopeprediction/2.2.2dev/output" target="_blank">documentation</a>.
-
-custom_logo: "nf-core-epitopeprediction_logo_light.png"
-custom_logo_url: https://github.com/nf-core/epitopeprediction/
-custom_logo_title: "nf-core/epitopeprediction"
-
+ <a href="https://nf-co.re/epitopeprediction/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
  "nf-core-epitopeprediction-methods-description":
  order: -1000