initial template build from nf-core/tools, version 3.0.2

.editorconfig

@@ -0,0 +1,32 @@
+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
+
+
+
+# ignore python and markdown
+[*.{py,md}]
+indent_style = unset

.gitignore

@@ -0,0 +1,9 @@
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
+null/

.gitpod.yml

@@ -0,0 +1,17 @@
+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
+    #- esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
+    - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
+    - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
+    - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
+    - nextflow.nextflow # Nextflow syntax highlighting
+    - oderwat.indent-rainbow # Highlight indentation level
+    - streetsidesoftware.code-spell-checker # Spelling checker for source code
+    - charliermarsh.ruff # Code linter Ruff

.nf-core.yml

@@ -0,0 +1,107 @@
+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
+  - conf/igenomes.config
+  - conf/igenomes_ignored.config
+  - conf/igenomes.config
+  - assets/email_template.html
+  - assets/sendmail_template.txt
+  - assets/email_template.txt
+  - .github/ISSUE_TEMPLATE/bug_report.yml
+  - .github/ISSUE_TEMPLATE/feature_request.yml
+  - .github/PULL_REQUEST_TEMPLATE.md
+  - .github/CONTRIBUTING.md
+  - .github/.dockstore.yml
+  - conf/igenomes.config
+  - conf/igenomes_ignored.config
+  - assets/email_template.html
+  - assets/sendmail_template.txt
+  - assets/email_template.txt
+  - CODE_OF_CONDUCT.md
+  - assets/nf-core-longreadmag_logo_light.png
+  - docs/images/nf-core-longreadmag_logo_light.png
+  - docs/images/nf-core-longreadmag_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
+  - .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
+  - .prettierignore
+  - CODE_OF_CONDUCT.md
+  - assets/nf-core-longreadmag_logo_light.png
+  - docs/images/nf-core-longreadmag_logo_light.png
+  - docs/images/nf-core-longreadmag_logo_dark.png
+  - .github/ISSUE_TEMPLATE/bug_report.yml
+  included_configs: false
+  multiqc_config:
+  - report_comment
+  nextflow_config:
+  - process.cpus
+  - process.memory
+  - process.time
+  - custom_config
+  - params.custom_config_version
+  - params.custom_config_base
+  - 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: Jim Downie, Will Eagles, Noah Gettle
+  description: Construct MAGs from long reads.
+  force: true
+  is_nfcore: false
+  name: longreadmag
+  org: sanger-tol
+  outdir: .
+  skip_features:
+  - github
+  - igenomes
+  - github_badges
+  - nf_core_configs
+  - codespaces
+  - fastqc
+  - email
+  - adaptivecard
+  - slackreport
+  - seqera_platform
+  version: 1.0.0dev
+update: null

.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:
+          - prettier@3.2.5
+
+  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
+    rev: "3.0.3"
+    hooks:
+      - id: editorconfig-checker
+        alias: ec

.prettierignore

@@ -0,0 +1,10 @@
+
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+testing/
+testing*
+*.pyc
+bin/

.prettierrc.yml

@@ -0,0 +1 @@
+printWidth: 120

CHANGELOG.md

@@ -0,0 +1,16 @@
+# sanger-tol/longreadmag: Changelog
+
+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).
+
+## v1.0.0dev - [date]
+
+Initial release of sanger-tol/longreadmag, created with the [nf-core](https://nf-co.re/) template.
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`

CITATIONS.md

@@ -0,0 +1,39 @@
+# sanger-tol/longreadmag: Citations
+
+## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
+
+> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
+
+## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+
+> 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.
+
+## Pipeline tools
+
+
+
+- [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.
+
+## Software packaging/containerisation tools
+
+- [Anaconda](https://anaconda.com)
+
+  > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+
+- [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
+
+  > 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.
+
+- [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.

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) Jim Downie, Will Eagles, Noah Gettle
+
+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.

README.md

@@ -0,0 +1,84 @@
+
+
+# sanger-tol/longreadmag
+
+## Introduction
+
+**sanger-tol/longreadmag** 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 sanger-tol/longreadmag \
+   -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
+
+sanger-tol/longreadmag was originally written by Jim Downie, Will Eagles, Noah Gettle.
+
+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 sanger-tol/longreadmag for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+
+<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
+
+An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
+
+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).

assets/methods_description_template.yml

@@ -0,0 +1,29 @@
+id: "sanger-tol-longreadmag-methods-description"
+description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication."
+section_name: "sanger-tol/longreadmag Methods Description"
+section_href: "https://github.com/sanger-tol/longreadmag"
+plot_type: "html"
+## 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 '${workflow}' object
+data: |
+  <h4>Methods</h4>
+  <p>Data was processed using sanger-tol/longreadmag v${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. 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>
+    <ul>
+      ${nodoi_text}
+      <li>The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!</li>
+      <li>You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.</li>
+    </ul>
+  </div>