Initial commit

CHANGELOG.md

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+# nf-core/bacqc: 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).
+
+## v1.0dev - [date]
+
+Initial release of nf-core/bacqc, created with the [nf-core](https://nf-co.re/) template.
+
+### `Added`
+
+### `Fixed`
+
+### `Dependencies`
+
+### `Deprecated`

CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-co.re/join/slack). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct/][version]
+
+[homepage]: https://contributor-covenant.org
+[version]: https://www.contributor-covenant.org/version/1/4/code-of-conduct/

Dockerfile

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+FROM nfcore/base:1.12.1
+LABEL authors="Andries van Tonder" \
+      description="Docker image containing all software requirements for the nf-core/bacqc pipeline"
+
+# Install the conda environment
+COPY environment.yml /
+RUN conda env create --quiet -f /environment.yml && conda clean -a
+
+# Add conda installation dir to PATH (instead of doing 'conda activate')
+ENV PATH /opt/conda/envs/nf-core-bacqc-1.0dev/bin:$PATH
+
+# Dump the details of the installed packages to a file for posterity
+RUN conda env export --name nf-core-bacqc-1.0dev > nf-core-bacqc-1.0dev.yml
+
+# Instruct R processes to use these empty files instead of clashing with a local version
+RUN touch .Rprofile
+RUN touch .Renviron

LICENSE

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+MIT License
+
+Copyright (c) Andries van Tonder
+
+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

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+# ![nf-core/bacqc](docs/images/nf-core-bacqc_logo.png)
+
+**Pipeline for running QC on bacterial sequence data**.
+
+[![GitHub Actions CI Status](https://github.com/nf-core/bacqc/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/bacqc/actions)
+[![GitHub Actions Linting Status](https://github.com/nf-core/bacqc/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/bacqc/actions)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.04.0-brightgreen.svg)](https://www.nextflow.io/)
+
+[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg)](https://bioconda.github.io/)
+[![Docker](https://img.shields.io/docker/automated/nfcore/bacqc.svg)](https://hub.docker.com/r/nfcore/bacqc)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23bacqc-4A154B?logo=slack)](https://nfcore.slack.com/channels/bacqc)
+
+## Introduction
+
+<!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
+**nf-core/bacqc** is a bioinformatics best-practise analysis pipeline for
+
+The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
+
+## Quick Start
+
+1. Install [`nextflow`](https://nf-co.re/usage/installation)
+
+2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_
+
+3. Download the pipeline and test it on a minimal dataset with a single command:
+
+    ```bash
+    nextflow run nf-core/bacqc -profile test,<docker/singularity/podman/conda/institute>
+    ```
+
+    > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile <institute>` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment.
+
+4. Start running your own analysis!
+
+    <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
+
+    ```bash
+    nextflow run nf-core/bacqc -profile <docker/singularity/podman/conda/institute> --input '*_R{1,2}.fastq.gz' --genome GRCh37
+    ```
+
+See [usage docs](https://nf-co.re/bacqc/usage) for all of the available options when running the pipeline.
+
+## Pipeline Summary
+
+By default, the pipeline currently performs the following:
+
+<!-- TODO nf-core: Fill in short bullet-pointed list of default steps of pipeline -->
+
+* Sequencing quality control (`FastQC`)
+* Overall pipeline run summaries (`MultiQC`)
+
+## Documentation
+
+The nf-core/bacqc pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/bacqc/usage) and [output](https://nf-co.re/bacqc/output).
+
+<!-- TODO nf-core: Add a brief overview of what the pipeline does and how it works -->
+
+## Credits
+
+nf-core/bacqc was originally written by Andries van Tonder.
+
+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).
+
+For further information or help, don't hesitate to get in touch on the [Slack `#bacqc` channel](https://nfcore.slack.com/channels/bacqc) (you can join with [this invite](https://nf-co.re/join/slack)).
+
+## Citations
+
+<!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi. -->
+<!-- If you use  nf-core/bacqc for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+
+You can cite the `nf-core` publication as follows:
+
+> **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).
+> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ)
+
+In addition, references of tools and data used in this pipeline are as follows:
+
+<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->

assets/email_template.html

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+<html>
+<head>
+  <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="nf-core/bacqc: Pipeline for running QC on bacterial sequence data">
+  <title>nf-core/bacqc 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>nf-core/bacqc v${version}</h1>
+<h2>Run Name: $runName</h2>
+
+<% if (!success){
+    out << """
+    <div style="color: #a94442; background-color: #f2dede; border-color: #ebccd1; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        <h4 style="margin-top:0; color: inherit;">nf-core/bacqc execution completed unsuccessfully!</h4>
+        <p>The exit status of the task that caused the workflow execution to fail was: <code>$exitStatus</code>.</p>
+        <p>The full error message was:</p>
+        <pre style="white-space: pre-wrap; overflow: visible; margin-bottom: 0;">${errorReport}</pre>
+    </div>
+    """
+} else {
+    out << """
+    <div style="color: #3c763d; background-color: #dff0d8; border-color: #d6e9c6; padding: 15px; margin-bottom: 20px; border: 1px solid transparent; border-radius: 4px;">
+        nf-core/bacqc execution completed successfully!
+    </div>
+    """
+}
+%>
+
+<p>The workflow was completed at <strong>$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>nf-core/bacqc</p>
+<p><a href="https://github.com/nf-core/bacqc">https://github.com/nf-core/bacqc</a></p>
+
+</div>
+
+</body>
+</html>

assets/email_template.txt

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+----------------------------------------------------
+                                        ,--./,-.
+        ___     __   __   __   ___     /,-._.--~\\
+  |\\ | |__  __ /  ` /  \\ |__) |__         }  {
+  | \\| |       \\__, \\__/ |  \\ |___     \\`-._,-`-,
+                                        `._,._,'
+  nf-core/bacqc v${version}
+----------------------------------------------------
+
+Run Name: $runName
+
+<% if (success){
+    out << "## nf-core/bacqc execution completed successfully! ##"
+} else {
+    out << """####################################################
+## nf-core/bacqc execution completed unsuccessfully! ##
+####################################################
+The exit status of the task that caused the workflow execution to fail was: $exitStatus.
+The full error message was:
+
+${errorReport}
+"""
+} %>
+
+
+The workflow was completed at $dateComplete (duration: $duration)
+
+The command used to launch the workflow was as follows:
+
+  $commandLine
+
+
+
+Pipeline Configuration:
+-----------------------
+<% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %>
+
+--
+nf-core/bacqc
+https://github.com/nf-core/bacqc

assets/multiqc_config.yaml

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+report_comment: >
+    This report has been generated by the <a href="https://github.com/nf-core/bacqc" target="_blank">nf-core/bacqc</a>
+    analysis pipeline. For information about how to interpret these results, please see the
+    <a href="https://github.com/nf-core/bacqc" target="_blank">documentation</a>.
+report_section_order:
+    software_versions:
+        order: -1000
+    nf-core-bacqc-summary:
+        order: -1001
+
+export_plots: true

assets/sendmail_template.txt

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+To: $email
+Subject: $subject
+Mime-Version: 1.0
+Content-Type: multipart/related;boundary="nfcoremimeboundary"
+
+--nfcoremimeboundary
+Content-Type: text/html; charset=utf-8
+
+$email_html
+
+--nfcoremimeboundary
+Content-Type: image/png;name="nf-core-bacqc_logo.png"
+Content-Transfer-Encoding: base64
+Content-ID: <nfcorepipelinelogo>
+Content-Disposition: inline; filename="nf-core-bacqc_logo.png"
+
+<% out << new File("$projectDir/assets/nf-core-bacqc_logo.png").
+  bytes.
+  encodeBase64().
+  toString().
+  tokenize( '\n' )*.
+  toList()*.
+  collate( 76 )*.
+  collect { it.join() }.
+  flatten().
+  join( '\n' ) %>
+
+<%
+if (mqcFile){
+def mqcFileObj = new File("$mqcFile")
+if (mqcFileObj.length() < mqcMaxSize){
+out << """
+--nfcoremimeboundary
+Content-Type: text/html; name=\"multiqc_report\"
+Content-Transfer-Encoding: base64
+Content-ID: <mqcreport>
+Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\"
+
+${mqcFileObj.
+  bytes.
+  encodeBase64().
+  toString().
+  tokenize( '\n' )*.
+  toList()*.
+  collate( 76 )*.
+  collect { it.join() }.
+  flatten().
+  join( '\n' )}
+"""
+}}
+%>
+
+--nfcoremimeboundary--