nextflow-io · adamrtalbot · Nov 20, 2024 · Nov 14, 2024 · Nov 14, 2024 · Nov 14, 2024
diff --git a/docs/hello_nextflow/09_hello_nf-core.md b/docs/hello_nextflow/09_hello_nf-core.md
diff --git a/docs/hello_nextflow/img/nf-core-modules.png b/docs/hello_nextflow/img/nf-core-modules.png
diff --git a/docs/hello_nextflow/img/pipeline_schema.png b/docs/hello_nextflow/img/pipeline_schema.png
diff --git a/hello-nextflow/hello-nf-core/data/sequencer_samplesheet.csv b/hello-nextflow/hello-nf-core/data/sequencer_samplesheet.csv
@@ -0,0 +1,5 @@
+sample,sequencer,fastq_1,fastq_2
+SAMPLE1_PE,sequencer1,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz
+SAMPLE2_PE,sequencer2,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz
+SAMPLE3_SE,sequencer3,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,
+SAMPLE3_SE,sequencer3,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,
diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.editorconfig b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.editorconfig
@@ -0,0 +1,33 @@
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+indent_size = 4
+indent_style = space
+
+[*.{md,yml,yaml,html,css,scss,js}]
+indent_size = 2
+
+# These files are edited and tested upstream in nf-core/modules
+[/modules/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+
+[/assets/email*]
+indent_size = unset
+
+# ignore python and markdown
+[*.{py,md}]
+indent_style = unset
diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.nf-core.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.nf-core.yml
@@ -0,0 +1,104 @@
+bump_version: null
+lint:
+  files_exist:
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/ISSUE_TEMPLATE/feature_request.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/CONTRIBUTING.md
+    - .github/.dockstore.yml
+    - .github/workflows/branch.yml
+    - .github/workflows/ci.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - conf/igenomes.config
+    - conf/igenomes_ignored.config
+    - CITATIONS.md
+    - CHANGELOG.md
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/ISSUE_TEMPLATE/feature_request.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/CONTRIBUTING.md
+    - .github/.dockstore.yml
+    - .github/workflows/branch.yml
+    - .github/workflows/ci.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - conf/igenomes.config
+    - conf/igenomes_ignored.config
+    - CITATIONS.md
+    - CHANGELOG.md
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-myfirstpipeline_logo_light.png
+    - docs/images/nf-core-myfirstpipeline_logo_light.png
+    - docs/images/nf-core-myfirstpipeline_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+  files_unchanged:
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/ISSUE_TEMPLATE/feature_request.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - .github/CONTRIBUTING.md
+    - .github/.dockstore.yml
+    - .github/CONTRIBUTING.md
+    - .prettierignore
+    - .prettierignore
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/ISSUE_TEMPLATE/feature_request.yml
+    - .github/PULL_REQUEST_TEMPLATE.md
+    - .github/workflows/branch.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - .github/CONTRIBUTING.md
+    - .github/.dockstore.yml
+    - .github/CONTRIBUTING.md
+    - .prettierignore
+    - .prettierignore
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-myfirstpipeline_logo_light.png
+    - docs/images/nf-core-myfirstpipeline_logo_light.png
+    - docs/images/nf-core-myfirstpipeline_logo_dark.png
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+  multiqc_config:
+    - report_comment
+  nextflow_config:
+    - manifest.name
+    - manifest.homePage
+    - validation.help.beforeText
+    - validation.help.afterText
+    - validation.summary.beforeText
+    - validation.summary.afterText
+  readme:
+    - nextflow_badge
+    - nextflow_badge
+    - nextflow_badge
+nf_core_version: 3.0.2
+org_path: null
+repository_type: pipeline
+template:
+  author: gitpod
+  description: My first pipeline
+  force: true
+  is_nfcore: false
+  name: myfirstpipeline
+  org: myorg
+  outdir: .
+  skip_features:
+    - github
+    - ci
+    - igenomes
+    - github_badges
+    - citations
+    - gitpod
+    - codespaces
+    - fastqc
+    - changelog
+    - adaptivecard
+    - slackreport
+  version: 1.0.0dev
+update: null
diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.pre-commit-config.yaml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.pre-commit-config.yaml
@@ -0,0 +1,13 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.1.0"
+    hooks:
+      - id: prettier
+        additional_dependencies:
+          - [email protected]
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "3.0.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec
diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierignore b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierignore
@@ -0,0 +1,10 @@
+email_template.html
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
+bin/
diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierrc.yml b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/.prettierrc.yml
@@ -0,0 +1 @@
+printWidth: 120
diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/LICENSE b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/LICENSE
@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) gitpod
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/README.md b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/README.md
@@ -0,0 +1,77 @@
+# myorg/myfirstpipeline
+
+## Introduction
+
+**myorg/myfirstpipeline** is a bioinformatics pipeline that ...
+
+<!-- TODO nf-core:
+   Complete this sentence with a 2-3 sentence summary of what types of data the pipeline ingests, a brief overview of the
+   major pipeline sections and the types of output it produces. You're giving an overview to someone new
+   to nf-core here, in 15-20 seconds. For an example, see https://github.com/nf-core/rnaseq/blob/master/README.md#introduction
+-->
+
+<!-- TODO nf-core: Include a figure that guides the user through the major workflow steps. Many nf-core
+     workflows use the "tube map" design for that. See https://nf-co.re/docs/contributing/design_guidelines#examples for examples.   -->
+<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
+
+2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+
+## Usage
+
+> [!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.
+
+<!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
+     Explain what rows and columns represent. For instance (please edit as appropriate):
+
+First, prepare a samplesheet with your input data that looks as follows:
+
+`samplesheet.csv`:
+
+```csv
+sample,fastq_1,fastq_2
+CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz
+```
+
+Each row represents a fastq file (single-end) or a pair of fastq files (paired end).
+
+-->
+
+Now, you can run the pipeline using:
+
+<!-- TODO nf-core: update the following command to include all required parameters for a minimal example -->
+
+```bash
+nextflow run myorg/myfirstpipeline \
+   -profile <docker/singularity/.../institute> \
+   --input samplesheet.csv \
+   --outdir <OUTDIR>
+```
+
+> [!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/docs/usage/getting_started/configuration#custom-configuration-files).
+
+## Credits
+
+myorg/myfirstpipeline was originally written by gitpod.
+
+We thank the following people for their extensive assistance in the development of this pipeline:
+
+<!-- TODO nf-core: If applicable, make list of people who have also contributed -->
+
+## Contributions and Support
+
+If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+
+## Citations
+
+<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
+<!-- If you use myorg/myfirstpipeline for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+
+This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).
+
+> **The nf-core framework for community-curated bioinformatics pipelines.**
+>
+> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
+>
+> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).
diff --git a/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/email_template.html b/hello-nextflow/hello-nf-core/solution/myorg-myfirstpipeline/assets/email_template.html
@@ -0,0 +1,110 @@
+<html>
+  <head>
+    <meta charset="utf-8" />
+    <meta http-equiv="X-UA-Compatible" content="IE=edge" />
+    <meta name="viewport" content="width=device-width, initial-scale=1" />
+
+    <meta name="description" content="myorg/myfirstpipeline: My first pipeline" />
+    <title>myorg/myfirstpipeline Pipeline Report</title>
+  </head>
+  <body>
+    <div style="font-family: Helvetica, Arial, sans-serif; padding: 30px; max-width: 800px; margin: 0 auto">
+      <img src="cid:nfcorepipelinelogo" />
+
+      <h1>myorg/myfirstpipeline ${version}</h1>
+      <h2>Run Name: $runName</h2>
+
+      <% if (!success){ out << """
+      <div
+        style="
+          color: #a94442;
+          background-color: #f2dede;
+          border-color: #ebccd1;
+          padding: 15px;
+          margin-bottom: 20px;
+          border: 1px solid transparent;
+          border-radius: 4px;
+        "
+      >
+        <h4 style="margin-top: 0; color: inherit">myorg/myfirstpipeline execution completed unsuccessfully!</h4>
+        <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
+        <p>The full error message was:</p>
+        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0">${errorReport}</pre>
+      </div>
+      """ } else { out << """
+      <div
+        style="
+          color: #3c763d;
+          background-color: #dff0d8;
+          border-color: #d6e9c6;
+          padding: 15px;
+          margin-bottom: 20px;
+          border: 1px solid transparent;
+          border-radius: 4px;
+        "
+      >
+        myorg/myfirstpipeline execution completed successfully!
+      </div>
+      """ } %>
+
+      <p>The workflow was completed at <strong>$dateComplete</strong> (duration: <strong>$duration</strong>)</p>
+      <p>The command used to launch the workflow was as follows:</p>
+      <pre
+        style="
+          white-space: pre-wrap;
+          overflow: visible;
+          background-color: #ededed;
+          padding: 15px;
+          border-radius: 4px;
+          margin-bottom: 30px;
+        "
+      >
+$commandLine</pre
+      >
+
+      <h3>Pipeline Configuration:</h3>
+      <table
+        style="
+          width: 100%;
+          max-width: 100%;
+          border-spacing: 0;
+          border-collapse: collapse;
+          border: 0;
+          margin-bottom: 30px;
+        "
+      >
+        <tbody style="border-bottom: 1px solid #ddd">
+          <% out << summary.collect{ k,v -> "
+          <tr>
+            <th
+              style="
+                text-align: left;
+                padding: 8px 0;
+                line-height: 1.42857143;
+                vertical-align: top;
+                border-top: 1px solid #ddd;
+              "
+            >
+              $k
+            </th>
+            <td
+              style="
+                text-align: left;
+                padding: 8px;
+                line-height: 1.42857143;
+                vertical-align: top;
+                border-top: 1px solid #ddd;
+              "
+            >
+              <pre style="white-space: pre-wrap; overflow: visible">$v</pre>
+            </td>
+          </tr>
+          " }.join("\n") %>
+        </tbody>
+      </table>
+
+      <p>myorg/myfirstpipeline</p>
+      <p><a href="https://github.com/myorg/myfirstpipeline">https://github.com/myorg/myfirstpipeline</a></p>
+    </div>
+  </body>
+</html>