Merge pull request #82 from nf-core/dev

Dev > Master for v2.1.0
nf-core · Nov 14, 2023 · 04f7539 · 04f7539
2 parents a797392 + 6591773
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diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {

diff --git a/.github/CONTRIBUTING.md b/.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
 
@@ -116,4 +118,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)
diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml
@@ -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)_

diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -14,18 +14,24 @@ 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: ${{ secrets.TOWER_COMPUTE_ENV }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/crisprseq/work-${{ github.sha }}/targeted_test
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/crisprseq/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-${{ github.sha }}/targeted_test"
             }
           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
diff --git a/.github/workflows/awsfulltest_screening.yml b/.github/workflows/awsfulltest_screening.yml
@@ -14,18 +14,22 @@ 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: ${{ secrets.TOWER_COMPUTE_ENV }}
-          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/crisprseq/work-${{ github.sha }}/screening_test
+          revision: ${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/crisprseq/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-${{ github.sha }}/screening_test"
             }
           profiles: test_screening_full
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -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/crisprseq/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-test-${{ github.sha }}"
             }
           profiles: test
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json
diff --git a/.github/workflows/linting.yml b/.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

diff --git a/.github/workflows/release-announcments.yml b/.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 }}
+          #
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -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

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,4 +1,6 @@
 repository_type: pipeline
 lint:
-  # We skip these linting as we have splitted tests between targeted and screening
-  files_exist: conf/test.config
+  files_exist:
+    - conf/test.config # We skip these linting as we have splitted tests between targeted and screening
+  files_unchanged:
+    - lib/NfcoreTemplate.groovy # Introduced a change ahead of the nf-core/tools release
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,11 +3,33 @@
 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).
 
+## [v2.1.0 - Jamon Salas](https://github.com/nf-core/crisprseq/releases/tag/2.1.0) - [14.11.2023]
+
+### Added
+
+- 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))
+- Template update v2.10 ([#79](https://github.com/nf-core/crisprseq/pull/79))
+
+### Fixed
+
+- Change to `process_high` for the mageck mle module ([#60](https://github.com/nf-core/crisprseq/pull/60))
+- Fix paired-end samplesheet file for screening ([#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))
+- Fix modules `BWA_INDEX` and `BOWTIE2_BUILD` after module update, new versions accept a meta map ([#76](https://github.com/nf-core/crisprseq/pull/76))
+- Update targeted metromap ([#78](https://github.com/nf-core/crisprseq/pull/78))
+
+### Deprecated
+
 ## [v2.0.0 - Paprika Lovelace](https://github.com/nf-core/crisprseq/releases/tag/2.0.0) - [05.07.2023]
 
 ### Added
 
-- Crisprseq screening analysis : mageck mle, mageck rra, mageck count and crisprcleanr-normalize ([#22]https://github.com/nf-core/crisprseq/pull/22))
+- Crisprseq screening analysis : mageck mle, mageck rra, mageck count and crisprcleanr-normalize ([#22](https://github.com/nf-core/crisprseq/pull/22))
 - Add new parameter `--analysis` to select analysis type (screening/targeted) ([#27](https://github.com/nf-core/crisprseq/pull/27))
 - Tests to run screening analysis ([#926]https://github.com/nf-core/test-datasets/pull/926)
 - Metro map for targeted analysis ([#35](https://github.com/nf-core/crisprseq/pull/35))

diff --git a/CITATIONS.md b/CITATIONS.md
@@ -16,6 +16,8 @@
 
 - [FastQC](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/)
 
   > 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.
@@ -61,11 +63,18 @@
 
   > 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.
 
 - [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.