Merge pull request #41 from nf-core/dev

Dev > Master for v2.0.0

.editorconfig

@@ -8,7 +8,7 @@ trim_trailing_whitespace = true
 indent_size = 4
 indent_style = space
 
-[*.{md,yml,yaml,html,css,scss,js,cff}]
+[*.{md,yml,yaml,html,css,scss,js}]
 indent_size = 2
 
 # These files are edited and tested upstream in nf-core/modules

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -45,6 +45,6 @@ body:
         * Nextflow version _(eg. 22.10.1)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
-        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_
+        * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_
         * OS _(eg. CentOS Linux, macOS, Linux Mint)_
         * Version of nf-core/crisprseq _(eg. 1.1, 1.5, 1.8.2)_

.github/PULL_REQUEST_TEMPLATE.md

@@ -15,7 +15,8 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/cris
 
 - [ ] This comment contains a description of changes (with reason).
 - [ ] If you've fixed a bug or added code that should be tested, add tests!
-- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/crisprseq/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/crisprseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
+- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/crisprseq/tree/master/.github/CONTRIBUTING.md)
+- [ ] If necessary, also make a PR on the nf-core/crisprseq _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.

.github/workflows/awsfulltest.yml

@@ -1,4 +1,4 @@
-name: nf-core AWS full size tests
+name: nf-core AWS full size tests targeted
 # This workflow is triggered on published releases.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
@@ -19,12 +19,12 @@ jobs:
           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-${{ github.sha }}
+          workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/crisprseq/work-${{ github.sha }}/targeted_test
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-${{ github.sha }}"
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-${{ github.sha }}/targeted_test"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/awsfulltest_screening.yml

@@ -0,0 +1,31 @@
+name: nf-core AWS full size tests screening
+# This workflow is triggered on published releases.
+# It can be additionally triggered manually with GitHub actions workflow dispatch button.
+# It runs the -profile 'test_full' on AWS batch
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+jobs:
+  run-tower:
+    name: Run AWS full tests
+    if: github.repository == 'nf-core/crisprseq'
+    runs-on: ubuntu-latest
+    steps:
+      - name: Launch workflow via tower
+        uses: nf-core/tower-action@v3
+        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-${{ github.sha }}/screening_test
+          parameters: |
+            {
+              "outdir": "s3://${{ 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

.github/workflows/awstest.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: nf-core/tower-action@v3
+        uses: seqeralabs/action-tower-launch@v1
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -22,7 +22,7 @@ jobs:
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

.github/workflows/branch.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Check PRs
         if: github.repository == 'nf-core/crisprseq'
         run: |
-          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/crisprseq ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
+          { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/crisprseq ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]]
 
       # If the above check failed, post a comment on the PR explaining the failure
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets

.github/workflows/ci.yml

@@ -24,8 +24,12 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
+        ANALYSIS:
+          - "test_screening"
+          - "test_targeted"
+          - "test_umis"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@v3
@@ -35,9 +39,6 @@ jobs:
         with:
           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
+      - name: Run pipeline with test data (${{ matrix.ANALYSIS }})
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.ANALYSIS }},docker --outdir ./results_${{ matrix.ANALYSIS }}

.github/workflows/clean-up.yml

@@ -0,0 +1,24 @@
+name: "Close user-tagged issues and PRs"
+on:
+  schedule:
+    - cron: "0 0 * * 0" # Once a week
+
+jobs:
+  clean-up:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v7
+        with:
+          stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
+          stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
+          close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled for 20 days with no activity."
+          days-before-stale: 30
+          days-before-close: 20
+          days-before-pr-close: -1
+          any-of-labels: "awaiting-changes,awaiting-feedback"
+          exempt-issue-labels: "WIP"
+          exempt-pr-labels: "WIP"
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"

.github/workflows/linting.yml

@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.7"
+          python-version: "3.8"
           architecture: "x64"
 
       - name: Install dependencies

.nf-core.yml

@@ -1 +1,4 @@
 repository_type: pipeline
+lint:
+  # We skip these linting as we have splitted tests between targeted and screening
+  files_exist: conf/test.config

.pre-commit-config.yaml

@@ -0,0 +1,13 @@
+repos:
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v2.7.1"
+    hooks:
+      - id: prettier

CHANGELOG.md

@@ -3,6 +3,26 @@
 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).
 
+## [v2.0.0 - 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))
+- 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))
+- Add new parameters `--reference` and `--protospacer` ([#45](https://github.com/nf-core/crisprseq/pull/45))
+- Add UMI clustering to crisprseq-targeted ([#24](https://github.com/nf-core/crisprseq/pull/24))
+- Template update v2.8 ([#21](https://github.com/nf-core/crisprseq/pull/21))
+
+### Fixed
+
+- Fix warning "module used more than once" ([#25](https://github.com/nf-core/crisprseq/pull/25))
+- Remove profile `aws_tower`, update from nf-core/tools v2.9 to make full tests pass ([#50](https://github.com/nf-core/crisprseq/pull/50))
+- Remove `quay.io` from all containers ([#50](https://github.com/nf-core/crisprseq/pull/50))
+- Fix resources on test screening full ([#50](https://github.com/nf-core/crisprseq/pull/56))
+- Fix id in crisprcleanr-normalize ([#50](https://github.com/nf-core/crisprseq/pull/56))
+
 ## [v1.0 - Salted Hypatia](https://github.com/nf-core/crisprseq/releases/tag/1.0) - [02.02.2023]
 
 Initial release of nf-core/crisprseq, created with the [nf-core](https://nf-co.re/) template.

CITATIONS.md

@@ -8,6 +8,10 @@
 
 > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
 
+## [Crispr-Analytics](https://doi.org/10.1371/journal.pcbi.1011137)
+
+> Sanvicente-García M, García-Valiente A, Jouide S, Jaraba-Wallace J, Bautista E, Escobosa M, et al. (2023) CRISPR-Analytics (CRISPR-A): A platform for precise analytics and simulations for gene editing. PLoS Comput Biol 19(5): e1011137. https://doi.org/10.1371/journal.pcbi.1011137
+
 ## Pipeline tools
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
@@ -49,6 +53,14 @@
 
   > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
 
+- [MAGeCK](https://pubmed.ncbi.nlm.nih.gov/25476604/)
+
+  > Li W, Xu H, Xiao T, Cong L, Love MI, Zhang F, Irizarry RA, Liu JS, Brown M, Liu XS. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 2014;15(12):554.
+
+- [CRISPRcleanR](https://pubmed.ncbi.nlm.nih.gov/30103702/)
+
+  > 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).
+
 - [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.