add Zenodo badge to README (6c749ea9) · Commits · github_fork / Universc

README.Rmd

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		![GitHub repo size](https://img.shields.io/github/repo-size/minoda-lab/universc)
		![GitHub top language](https://img.shields.io/github/languages/top/minoda-lab/universc)
		![GitHub language count](https://img.shields.io/github/languages/count/minoda-lab/universc)
		[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7116956.svg)](https://doi.org/10.5281/zenodo.7116956)

		![GitHub all releases](https://img.shields.io/github/downloads/minoda-lab/universc/total?label=GitHub%20downloads)
		![GitHub release (latest by date)](https://img.shields.io/github/v/release/minoda-lab/universc?label=GitHub%20release)
		@@ -136,6 +137,18 @@ Once you have a docker image installed on your system, you can run the applicabl

		[https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_app_release/](https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_app_release/)

		### Nextflow users

		A [nextflow](https://www.nextflow.io/) custom [module](https://nf-co.re/modules) is being developed for the [nf-core](https://nf-co.re) community. It will be available to use in nf-core [pipelines](https://nf-co.re/pipelines).

		See the issue and pull request for details:

		[https://github.com/nf-core/modules/issues/1644](https://github.com/nf-core/modules/issues/1644)

		[https://github.com/nf-core/modules/pull/1706](https://github.com/nf-core/modules/pull/1706)

		We plan to make this available in the near future. If you are interested in using it or contributing to development, please contact the maintainers. Thank you!

		## Purpose

		We've developed a bash script that will run Cell Ranger on FASTQ files for these technologies. See below for details on how to use it.

README.html

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		<p><embed src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.3" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%22layers@1.2.3%22" alt="MicroBadger Layers (latest)" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.3?label=%22image%20size@1.2.3" /> <img src="https://img.shields.io/docker/v/tomkellygenetics/universc/latest" alt="Docker Image Version (latest by date)" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest" alt="MicroBadger Layers (latest)" /> <img src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/latest" alt="Docker Image Size (latest)" /></p>
		<p><img src="https://img.shields.io/github/checks-status/minoda-lab/universc/master?label=GitHub%20checks" alt="GitHub branch checks state" /> <img src="https://img.shields.io/github/release-date/minoda-lab/universc" alt="GitHub Release Date" /> <img src="https://img.shields.io/github/last-commit/minoda-lab/universc/master" alt="GitHub last commit (branch)" /> <img src="https://img.shields.io/github/issues/minoda-lab/universc" alt="GitHub issues" /> <img src="https://img.shields.io/github/issues-pr/minoda-lab/universc" alt="GitHub pull requests" /></p>
		<p><a href="http://hits.dwyl.com/minoda-lab/universc"><img src="http://hits.dwyl.com/minoda-lab/universc.svg" alt="GitHub Views" /></a> <a href="http://hits.dwyl.com/tomkellygenetics/universc"><img src="http://hits.dwyl.com/tomkellygenetics/universc.svg" alt="GitHub Views" /></a> <img src="https://img.shields.io/github/search/minoda-lab/universc/master" alt="GitHub search hit counter" /> <img src="https://img.shields.io/github/forks/minoda-lab/universc?style=social" alt="GitHub forks" /> <img src="https://img.shields.io/github/stars/minoda-lab/universc?style=social" alt="GitHub Repo stars" /> <img src="https://img.shields.io/github/watchers/minoda-lab/universc?style=social" alt="GitHub watchers" /></p>
		<p><img src="https://img.shields.io/github/languages/code-size/minoda-lab/universc" alt="GitHub code size in bytes" /> <img src="https://img.shields.io/github/repo-size/minoda-lab/universc" alt="GitHub repo size" /> <img src="https://img.shields.io/github/languages/top/minoda-lab/universc" alt="GitHub top language" /> <img src="https://img.shields.io/github/languages/count/minoda-lab/universc" alt="GitHub language count" /></p>
		<p><img src="https://img.shields.io/github/languages/code-size/minoda-lab/universc" alt="GitHub code size in bytes" /> <img src="https://img.shields.io/github/repo-size/minoda-lab/universc" alt="GitHub repo size" /> <img src="https://img.shields.io/github/languages/top/minoda-lab/universc" alt="GitHub top language" /> <img src="https://img.shields.io/github/languages/count/minoda-lab/universc" alt="GitHub language count" /> <a href="https://doi.org/10.5281/zenodo.7116956"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.7116956.svg" alt="Zenodo DOI" /></a></p>
		<p><img src="https://img.shields.io/github/downloads/minoda-lab/universc/total?label=GitHub%20downloads" alt="GitHub all releases" /> <img src="https://img.shields.io/github/v/release/minoda-lab/universc?label=GitHub%20release" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.2.3/total" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.2.3/total" alt="GitHub release (by tag)" /></p>
		<p><img src="https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg" alt="Docker CI" /> <img src="https://github.com/minoda-lab/universc/workflows/Docker%20compose%20build/badge.svg" alt="Docker compose" /> <img src="https://github.com/minoda-lab/universc/workflows/Docker%20container%20tests/badge.svg" alt="Actions Build" /> <img src="https://github.com/minoda-lab/universc/workflows/Docker%20build%20image/badge.svg" alt="Actions Call" /></p>
		<p><img src="https://github.com/minoda-lab/universc/workflows/Run%20all%20tests%20in%20Docker/badge.svg" alt="Actions Tests" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%2010x%20Genomics/badge.svg" alt="Test 10x Genomics" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20DropSeq%20%2F%20Nadia/badge.svg" alt="Test DropSeq" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20ICELL8/badge.svg" alt="Test ICELL8" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20SCI%2DSeq/badge.svg" alt="Test SCI-Seq" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20inDrops%20v3/badge.svg" alt="Test inDrops v3" /> <img src="https://github.com/minoda-lab/universc/workflows/Test%20Smart%2DSeq3/badge.svg" alt="Test Smart-Seq3" /></p>
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		<p>We also provide a graphical user interface (GUI) based application to run the Docker <a href="#Docker">image</a>. Please install Docker as described above and pull our <code>tomkellygenetics/universc:latest</code> image using either the docker command-line interface (CLI) or the docker graphical application.</p>
		<p>Once you have a docker image installed on your system, you can run the applicable binary available here:</p>
		<p><a href="https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_app_release/" class="uri">https://genomec.gsc.riken.jp/gerg/UniverSC/UniverSC_app_release/</a></p>
		<h3 id="nextflow-users">Nextflow users</h3>
		<p>A <a href="https://www.nextflow.io/">nextflow</a> custom <a href="https://nf-co.re/modules">module</a> is being developed for the <a href="https://nf-co.re">nf-core</a> community. It will be available to use in nf-core <a href="https://nf-co.re/pipelines">pipelines</a>.</p>
		<p>See the issue and pull request for details:</p>
		<p><a href="https://github.com/nf-core/modules/issues/1644" class="uri">https://github.com/nf-core/modules/issues/1644</a></p>
		<p><a href="https://github.com/nf-core/modules/pull/1706" class="uri">https://github.com/nf-core/modules/pull/1706</a></p>
		<p>We plan to make this available in the near future. If you are interested in using it or contributing to development, please contact the maintainers. Thank you!</p>
		<h2 id="purpose">Purpose</h2>
		<p>We've developed a bash script that will run Cell Ranger on FASTQ files for these technologies. See below for details on how to use it.</p>
		<p>If you use this tool, please <a href="#Citation">cite</a> to acknowledge the efforts of the authors. You can report problems and request new features to the maintainers with and <a href="#Issues">issue</a> on GitHub. Details on how to <a href="#Install">install</a> and <a href="#Usage">run</a> are provided below. Please see the <a href="#Help">help</a> and <a href="#Examples">examples</a> to try solve your problem before submitting an issue.</p>

README.md

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		index: 1
		- name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"
		index: 2
		date: "Monday 23 May 2022"
		date: "Wednesday 28 September 2022"
		output:
		prettydoc::html_pretty:
		theme: cayman
		@@ -58,6 +58,7 @@ tags:
		![GitHub repo size](https://img.shields.io/github/repo-size/minoda-lab/universc)
		![GitHub top language](https://img.shields.io/github/languages/top/minoda-lab/universc)
		![GitHub language count](https://img.shields.io/github/languages/count/minoda-lab/universc)
		[![Zenodo DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7116956.svg)](https://doi.org/10.5281/zenodo.7116956)

		![GitHub all releases](https://img.shields.io/github/downloads/minoda-lab/universc/total?label=GitHub%20downloads)
		![GitHub release (latest by date)](https://img.shields.io/github/v/release/minoda-lab/universc?label=GitHub%20release)
		@@ -142,9 +143,9 @@ A [nextflow](https://www.nextflow.io/) custom [module](https://nf-co.re/modules)

		See the issue and pull request for details:

		https://github.com/nf-core/modules/issues/1644
		[https://github.com/nf-core/modules/issues/1644](https://github.com/nf-core/modules/issues/1644)

		https://github.com/nf-core/modules/pull/1706
		[https://github.com/nf-core/modules/pull/1706](https://github.com/nf-core/modules/pull/1706)

		We plan to make this available in the near future. If you are interested in using it or contributing to development, please contact the maintainers. Thank you!

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