update documentation for 1.1.6

minoda-lab · Sep 26, 2021 · a24a656 · a24a656
1 parent 0221067
commit a24a656
Show file tree

Hide file tree

Showing 7 changed files with 49 additions and 39 deletions.
diff --git a/.version b/.version
@@ -1 +1 @@
-1.1.5
+1.1.6
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,3 +1,13 @@
+### 1.1.6
+
+- update building STAR in Docker containers
+
+- updates to syntax in script and subroutines
+
+- bug fixes to allow running without --verbose parameters
+
+- minor updates to documentation for added technologies
+
 ### 1.1.5
 
 - add subroutine to support custom references

diff --git a/README.Rmd b/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/1.1.5)
-![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].5")
-![Docker Image Size (v1.1.5)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.5?label="image%[email protected].5)
+![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.1.6)
+![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].6")
+![Docker Image Size (v1.1.6)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.6?label="image%[email protected].6)
 ![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)
@@ -61,8 +61,8 @@ 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/1.1.5/total)
-![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.5/total)
+![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6/total)
+![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6/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)
@@ -93,7 +93,7 @@ and use this tool to process single-cell RNA-Seq data from FASTQ format.
 
 **Package**
 
-UniverSC version 1.1.5
+UniverSC version 1.1.6
 
 **Maintainers**
 
@@ -346,21 +346,21 @@ as follows:
 
 Kelly, S.T., Battenberg, Hetherington, N.A., K., 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/10.11.1.5021.01.19.427209](https://doi.org/10.11.1.5021.01.19.427209)
-package version 1.1.5. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.11.1.6021.01.19.427209](https://doi.org/10.11.1.6021.01.19.427209)
+package version 1.1.6. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
 
 ```
 @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},
         elocation-id = {2021.01.19.427209},
         year = {2021},
-        doi = {10.11.1.5021.01.19.427209},
+        doi = {10.11.1.6021.01.19.427209},
         publisher = {Cold Spring Harbor Laboratory},
         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 1.1.5},
+        note = {package version 1.1.6},
         URL = {https://github.com/minoda-lab/universc},
 }
 
@@ -371,7 +371,7 @@ package version 1.1.5. [https://github.com/minoda-lab/universc](https://github.c
     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 = {2021},
-    note = {package version 1.1.5},
+    note = {package version 1.1.6},
     url = {https://github.com/minoda-lab/universc},
   }
 ```
@@ -824,7 +824,7 @@ your systems administrator.
 
 #### Pulling from remote DockerHub repository
 
-We provide a docker image for UniverSC version 1.1.5.
+We provide a docker image for UniverSC version 1.1.6.
 
 You can import it if you have docker installed.
 

diff --git a/README.html b/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/1.1.5" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%[email protected].5%22" alt="MicroBadger Layers (latest)" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.5?label=%22image%[email protected].5" /> <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/1.1.6" /> <img src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%[email protected].6%22" alt="MicroBadger Layers (latest)" /> <embed src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.1.6?label=%22image%[email protected].6" /> <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/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/1.1.5/total" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.1.5/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/1.1.6/total" alt="GitHub release (latest by date)" /> <img src="https://img.shields.io/github/downloads/minoda-lab/universc/1.1.6/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 1.1.5</p>
+<p>UniverSC version 1.1.6</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>
@@ -159,26 +159,26 @@ <h2 id="release">Release</h2>
 <p>We have tested it on several technologies but we need users like you to let us know how we can improve it. We hope that it will save you time by handing tedious parts of data formatting so that you can focus on the results.</p>
 <h3 id="citation">Citation <span id="Citation"><span></h3>
 <p>A submission to a journal and biorXiv is in progress. Please cite these when they are available. Currently, the package can be cited as follows:</p>
-<p>Kelly, S.T., Battenberg, Hetherington, N.A., K., 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/10.11.1.5021.01.19.427209" class="uri">https://doi.org/10.11.1.5021.01.19.427209</a> package version 1.1.5. <a href="https://github.com/minoda-lab/universc" class="uri">https://github.com/minoda-lab/universc</a></p>
+<p>Kelly, S.T., Battenberg, Hetherington, N.A., K., 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/10.11.1.6021.01.19.427209" class="uri">https://doi.org/10.11.1.6021.01.19.427209</a> package version 1.1.6. <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},
         elocation-id = {2021.01.19.427209},
         year = {2021},
-        doi = {10.11.1.5021.01.19.427209},
+        doi = {10.11.1.6021.01.19.427209},
         publisher = {Cold Spring Harbor Laboratory},
         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 1.1.5},
+        note = {package version 1.1.6},
         URL = {https://github.com/minoda-lab/universc},
 }
 </code></pre>
 <pre><code>@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 = {2021},
-    note = {package version 1.1.5},
+    note = {package version 1.1.6},
     url = {https://github.com/minoda-lab/universc},
   }</code></pre>
 <h3 id="bug-reports">Bug Reports <span id="Issues"><span></h3>
@@ -389,7 +389,7 @@ <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 1.1.5.</p>
+<p>We provide a docker image for UniverSC version 1.1.6.</p>
 <p>You can import it if you have docker installed.</p>
 <pre><code>docker pull tomkellygenetics/universc:latest</code></pre>
 <p>Then you can run UniverSC with:</p>