Merge remote-tracking branch 'source_repo/dev' into bump

.github/CONTRIBUTING.md

@@ -116,4 +116,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)

.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)_

.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-${{ github.sha }}
           parameters: |
             {
-              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-${{ github.sha }}/targeted_test"
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+              "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/crisprseq/results-${{ github.sha }}"
             }
           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

.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

.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

CHANGELOG.md

@@ -7,6 +7,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### 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))
+
 ### Fixed
 
 ### Deprecated

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]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+
 - [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.
@@ -67,5 +69,8 @@
 
 - [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.

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) mirpedrol
+Copyright (c) Júlia Mir Pedrol, Laurence Kuhlburger
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -99,11 +99,11 @@ nextflow run nf-core/crisprseq --input samplesheet.csv --analysis <targeted/scre
 > 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).
 
-For more details, please refer to the [usage documentation](https://nf-co.re/crisprseq/usage) and the [parameter documentation](https://nf-co.re/crisprseq/parameters).
+For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/crisprseq/usage) and the [parameter documentation](https://nf-co.re/crisprseq/parameters).
 
 ## Pipeline output
 
-To see the the results of a test run with a full size dataset refer to the [results](https://nf-co.re/crisprseq/results) tab on the nf-core website pipeline page.
+To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/crisprseq/results) tab on the nf-core website pipeline page.
 For more details about the output files and reports, please refer to the
 [output documentation](https://nf-co.re/crisprseq/output).
 

assets/email_template.html

@@ -4,7 +4,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/crisprseq: Pipeline for the analysis of crispr data">
+  <meta name="description" content="nf-core/crisprseq: Pipeline for the analysis of CRISPR data">
   <title>nf-core/crisprseq Pipeline Report</title>
 </head>
 <body>

assets/methods_description_template.yml

@@ -3,17 +3,21 @@ description: "Suggested text and references to use when describing pipeline usag
 section_name: "nf-core/crisprseq Methods Description"
 section_href: "https://github.com/nf-core/crisprseq"
 plot_type: "html"
-## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline
+## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using nf-core/crisprseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
+  <p>Data was processed using nf-core/crisprseq v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
+  <p>${tool_citations}</p>
   <h4>References</h4>
   <ul>
-    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
-    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
+    <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: <a href="https://doi.org/10.1038/nbt.3820">10.1038/nbt.3820</a></li>
+    <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: <a href="https://doi.org/10.1038/s41587-020-0439-x">10.1038/s41587-020-0439-x</a></li>
+    <li>Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: <a href="https://doi.org/10.1038/s41592-018-0046-7">10.1038/s41592-018-0046-7</a></li>
+    <li>da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: <a href="https://doi.org/10.1093/bioinformatics/btx192">10.1093/bioinformatics/btx192</a></li>
+    ${tool_bibliography}
   </ul>
   <div class="alert alert-info">
     <h5>Notes:</h5>

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
   This report has been generated by the <a href="https://github.com/nf-core/crisprseq" target="_blank">nf-core/crisprseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/crisprseq" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/crisprseq/2.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-crisprseq-methods-description":
     order: -1000

assets/schema_input.json

@@ -10,25 +10,44 @@
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "meta": ["id"]
             },
             "fastq_1": {
                 "type": "string",
+                "format": "file-path",
+                "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
             "fastq_2": {
+                "type": "string",
+                "format": "file-path",
+                "exists": true,
                 "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
-                "anyOf": [
-                    {
-                        "type": "string",
-                        "pattern": "^\\S+\\.f(ast)?q\\.gz$"
-                    },
-                    {
-                        "type": "string",
-                        "maxLength": 0
-                    }
-                ]
+                "pattern": "^\\S+\\.f(ast)?q\\.gz$"
+            },
+            "condition": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "enum": ["control", "treatment"],
+                "errorMessage": "Condition name must be one of 'control' or 'treatment'",
+                "meta": ["condition"]
+            },
+            "reference": {
+                "type": "string",
+                "pattern": "^[ACTGNactgn]+$",
+                "errorMessage": "Reference sequence must be a valid DNA sequence"
+            },
+            "protospacer": {
+                "type": "string",
+                "pattern": "^[ACTGNactgn]+$",
+                "errorMessage": "Protospacer sequence must be a valid DNA sequence"
+            },
+            "template": {
+                "type": "string",
+                "pattern": "^[ACTGNactgn]+$",
+                "errorMessage": "Template sequence must be a valid DNA sequence"
             }
         },
         "required": ["sample", "fastq_1"]

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+            "author_name": "nf-core/crisprseq v${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [