Merge branch 'dev' into metromap

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

CHANGELOG.md

@@ -9,10 +9,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - Template update v2.9 ([#52](https://github.com/nf-core/crisprseq/pull/52))
 - Use `Channel.fromSamplesheet()` from `nf-validation` to validate input sample sheets and create an input channel ([#58](https://github.com/nf-core/crisprseq/pull/58))
+- BAGEL2 as a module which detects gene essentiality ([#60](https://github.com/nf-core/crisprseq/pull/60))
 - Add custom plots to MultiQC report (cutadapt module, read processing, edition, edition QC) ([#64](https://github.com/nf-core/crisprseq/pull/64))
 
 ### Fixed
 
+- Change to `process_high` for the mageck mle module ([#60](https://github.com/nf-core/crisprseq/pull/60)
 - Summary processes don't modify the input file anymore, allowing resuming these processes ([#66](https://github.com/nf-core/crisprseq/pull/66))
 - Do not stash unexistent files, use empty lists instead. Fixes AWS tests ([#67](https://github.com/nf-core/crisprseq/pull/67))
 - Rename process `merging_summary` to `preprocessing_summary` to improve clarity ([#69](https://github.com/nf-core/crisprseq/pull/69))

CITATIONS.md

@@ -16,7 +16,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > 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/)
 
@@ -63,6 +63,10 @@
 
   > Li, W. et al. Quality control, modeling, and visualization of CRISPR screens with MAGeCK-VISPR. Genome Biology 16, 281, doi:10.1186/s13059-015-0843-6 (2015).
 
+- [BAGEL2](https://pubmed.ncbi.nlm.nih.gov/33407829/)
+
+  > Kim E, Hart T. Improved analysis of CRISPR fitness screens and reduced off-target effects with the BAGEL2 gene essentiality classifier. Genome Med. 2021 Jan 6;13(1):2. doi: 10.1186/s13073-020-00809-3. PMID: 33407829; PMCID: PMC7789424.
+
 - [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
 
   > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.