update documentation for 1.2.5.1 (minor patch reverting partial changes)

.version

@@ -1 +1 @@
-1.2.5
+1.2.5.1

CHANGELOG

@@ -1,3 +1,7 @@
+### 1.2.5.1
+
+- minor patch to revert potentially breaking changes in v1.2.5 when running perl instead of sed 
+
 ### 1.2.5
 
 - updates PATH environment variable to call /universc/launch_universc.sh from any working directory

CITATION.cff

@@ -11,7 +11,7 @@ authors:
   email: "[email protected]"
   affiliation: "Center for Sustainable Resource Science, RIKEN, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Japan"
   orcid: "http://orcid.org/0000-0001-7517-2657"
-version: 1.2.5
+version: 1.2.5.1
 doi: 10.1101/2021.01.19.427209
 date-released: 2021-02-14
 url: "https://github.com/minoda-lab/universc"

README.Rmd

@@ -34,9 +34,9 @@ tags:
 ![Docker Stars](https://img.shields.io/docker/stars/tomkellygenetics/universc)
 ![Docker Pulls](https://img.shields.io/docker/pulls/tomkellygenetics/universc)
 
-![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.5)
-![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected]")
-![Docker Image Size (v1.2.5)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5?label="image%[email protected])
+![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.5.1)
+![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].1")
+![Docker Image Size (v1.2.5.1)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5.1?label="image%[email protected].1)
 ![Docker Image Version (latest by date)](https://img.shields.io/docker/v/tomkellygenetics/universc/latest)
 ![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest)
 ![Docker Image Size (latest)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/latest)
@@ -62,8 +62,8 @@ tags:
 
 ![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)
-![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.5/total)
-![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.5/total)
+![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.5.1/total)
+![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.5.1/total)
 
 ![Docker CI](https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg)
 ![Docker compose](https://github.com/minoda-lab/universc/workflows/Docker%20compose%20build/badge.svg)
@@ -94,7 +94,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format.
 
 **Package**
 
-UniverSC version 1.2.5
+UniverSC version 1.2.5.1
 
 **Maintainers**
 
@@ -377,7 +377,7 @@ A flexible cross-platform single-cell data processing pipeline. _Nat Commun_ **1
         number="1",
         pages="1-7",
         month="Nov",
-        note = {https://github.com/minoda-lab/universc package version 1.2.5},
+        note = {https://github.com/minoda-lab/universc package version 1.2.5.1},
         URL = {https://doi.org/10.1038/s41467-022-34681-z}
 }
 ```
@@ -387,7 +387,7 @@ The preprint can also be found here:
 Kelly, S.T., Battenberg K., Hetherington, N.A., Hayashi, K., and Minoda, A. (2021)
 UniverSC: a flexible cross-platform single-cell data processing pipeline.
 bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)
-package version 1.2.5. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+package version 1.2.5.1. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
 
 ```
 @article {Kelly2021.01.19.427209,
@@ -400,7 +400,7 @@ package version 1.2.5. [https://github.com/minoda-lab/universc](https://github.c
         abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},
         eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},
         journal = {{bioRxiv}},
-        note = {package version 1.2.5},
+        note = {package version 1.2.5.1},
         URL = {https://github.com/minoda-lab/universc},
 }
 
@@ -414,7 +414,7 @@ The software can also be cited directly as a manual:
     title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},
     author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},
     year = {2023},
-    note = {package version 1.2.5},
+    note = {package version 1.2.5.1},
     url = {https://github.com/minoda-lab/universc},
   }
 ```
@@ -867,7 +867,7 @@ your systems administrator.
 
 #### Pulling from remote DockerHub repository
 
-We provide a docker image for UniverSC version 1.2.5.
+We provide a docker image for UniverSC version 1.2.5.1.
 
 You can import it if you have docker installed.
 

README.html

@@ -1,9 +1,9 @@
 <p><img src="https://img.shields.io/docker/automated/tomkellygenetics/universc?label=docker%20local%20build" alt="Docker Manual build" /> <img src="https://img.shields.io/docker/cloud/automated/tomkellygenetics/universc?label=docker%20cloud%20build" alt="Docker Cloud Build" /> <img src="https://img.shields.io/docker/cloud/build/tomkellygenetics/universc?label=cloud%20build" alt="Docker Cloud Status" /> <img src="https://img.shields.io/docker/stars/tomkellygenetics/universc" alt="Docker Stars" /> <img src="https://img.shields.io/docker/pulls/tomkellygenetics/universc" alt="Docker Pulls" /></p>
-<p><embed src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.5" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%[email protected]%22" alt="MicroBadger Layers (latest)" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5?label=%22image%[email protected]" /> <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><embed src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.5.1" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%[email protected].1%22" alt="MicroBadger Layers (latest)" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.5.1?label=%22image%[email protected].1" /> <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" /> <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/1.2.5/total" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.2.5/total" alt="GitHub release (by tag)" /></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/1.2.5.1/total" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.2.5.1/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>
 <h1 id="universc">UniverSC</h1>
@@ -12,7 +12,7 @@ <h1 id="universc">UniverSC</h1>
 <p><strong>Summary</strong></p>
 <p>Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. UniverSC is a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms. Here we provide a guide to install and use this tool to process single-cell RNA-Seq data from FASTQ format.</p>
 <p><strong>Package</strong></p>
-<p>UniverSC version 1.2.5</p>
+<p>UniverSC version 1.2.5.1</p>
 <p><strong>Maintainers</strong></p>
 <p>Tom Kelly<sup>†</sup> (RIKEN IMS) and Kai Battenberg<sup>†</sup> (RIKEN CSRS/IMS)</p>
 <p>† These authors contributed equally to this work</p>
@@ -179,11 +179,11 @@ <h3 id="citation">Citation <span id="Citation"><span></h3>
         number=&quot;1&quot;,
         pages=&quot;1-7&quot;,
         month=&quot;Nov&quot;,
-        note = {https://github.com/minoda-lab/universc package version 1.2.5},
+        note = {https://github.com/minoda-lab/universc package version 1.2.5.1},
         URL = {https://doi.org/10.1038/s41467-022-34681-z}
 }</code></pre>
 <p>The preprint can also be found here:</p>
-<p>Kelly, S.T., Battenberg K., Hetherington, N.A., Hayashi, K., and Minoda, A. (2021) UniverSC: a flexible cross-platform single-cell data processing pipeline. bioRxiv 2021.01.19.427209; doi: <a href="https://doi.org/10.1101/2021.01.19.427209" class="uri">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.2.5. <a href="https://github.com/minoda-lab/universc" class="uri">https://github.com/minoda-lab/universc</a></p>
+<p>Kelly, S.T., Battenberg K., Hetherington, N.A., Hayashi, K., and Minoda, A. (2021) UniverSC: a flexible cross-platform single-cell data processing pipeline. bioRxiv 2021.01.19.427209; doi: <a href="https://doi.org/10.1101/2021.01.19.427209" class="uri">https://doi.org/10.1101/2021.01.19.427209</a> package version 1.2.5.1. <a href="https://github.com/minoda-lab/universc" class="uri">https://github.com/minoda-lab/universc</a></p>
 <pre><code>@article {Kelly2021.01.19.427209,
         author = {Kelly, S. Thomas and Battenberg, Kai and Hetherington, Nicola A. and Hayashi, Makoto and Minoda, Aki},
         title = {{UniverSC}: a flexible cross-platform single-cell data processing pipeline},
@@ -194,7 +194,7 @@ <h3 id="citation">Citation <span id="Citation"><span></h3>
         abstract = {Single-cell RNA-sequencing analysis to quantify RNA molecules in individual cells has become popular owing to the large amount of information one can obtain from each experiment. We have developed UniverSC (https://github.com/minoda-lab/universc), a universal single-cell processing tool that supports any UMI-based platform. Our command-line tool enables consistent and comprehensive integration, comparison, and evaluation across data generated from a wide range of platforms.Competing Interest StatementThe authors have declared no competing interest.},
         eprint = {https://www.biorxiv.org/content/early/2021/01/19/2021.01.19.427209.full.pdf},
         journal = {{bioRxiv}},
-        note = {package version 1.2.5},
+        note = {package version 1.2.5.1},
         URL = {https://github.com/minoda-lab/universc},
 }
 </code></pre>
@@ -203,7 +203,7 @@ <h3 id="citation">Citation <span id="Citation"><span></h3>
     title = {{UniverSC}:  a flexible cross-platform single-cell data processing pipeline},
     author = {S. Thomas Kelly, Kai Battenberg, Nicola A. Hetherington, Makoto Hayashi, and Aki Minoda},
     year = {2023},
-    note = {package version 1.2.5},
+    note = {package version 1.2.5.1},
     url = {https://github.com/minoda-lab/universc},
   }</code></pre>
 <h3 id="bug-reports">Bug Reports <span id="Issues"><span></h3>
@@ -414,7 +414,7 @@ <h3 id="docker-image">Docker image <span id="Docker"><span></h3>
 <pre><code>docker login -u &quot;myusername&quot;</code></pre>
 <p>If you cannot run docker on a remote server, contact your systems administrator.</p>
 <h4 id="pulling-from-remote-dockerhub-repository">Pulling from remote DockerHub repository</h4>
-<p>We provide a docker image for UniverSC version 1.2.5.</p>
+<p>We provide a docker image for UniverSC version 1.2.5.1.</p>
 <p>You can import it if you have docker installed.</p>
 <pre><code>docker pull tomkellygenetics/universc:latest</code></pre>
 <h4 id="running-processes-in-a-docker-container">Running processes in a docker container</h4>