update documentation for 1.2.7

minoda-lab · Feb 6, 2024 · 0666845 · 0666845
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diff --git a/.version b/.version
@@ -1 +1 @@
-1.2.6
+1.2.7
diff --git a/CITATION.cff b/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: 1.2.6
+version: 1.2.7
 doi: 10.1101/2021.01.19.427209
 date-released: 2021-02-14
 url: "https://github.com/minoda-lab/universc"

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/1.2.6)
-![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].6")
-![Docker Image Size (v1.2.6)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.6?label="image%[email protected].6)
+![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.7)
+![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].7")
+![Docker Image Size (v1.2.7)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.7?label="image%[email protected].7)
 ![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/1.2.6/total)
-![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.6/total)
+![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.7/total)
+![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.7/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 1.2.6
+UniverSC version 1.2.7
 
 **Maintainers**
 
@@ -391,7 +391,7 @@ 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 1.2.6},
+        note = {https://github.com/minoda-lab/universc package version 1.2.7},
         URL = {https://doi.org/10.1038/s41467-022-34681-z}
 }
 ```
@@ -401,7 +401,7 @@ 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 1.2.6. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+package version 1.2.7. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
 
 ```
 @article {Kelly2021.01.19.427209,
@@ -414,7 +414,7 @@ package version 1.2.6. [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 1.2.6},
+        note = {package version 1.2.7},
         URL = {https://github.com/minoda-lab/universc},
 }
 
@@ -428,7 +428,7 @@ 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 1.2.6},
+    note = {package version 1.2.7},
     url = {https://github.com/minoda-lab/universc},
   }
 ```
@@ -881,7 +881,7 @@ your systems administrator.
 
 #### Pulling from remote DockerHub repository
 
-We provide a docker image for UniverSC version 1.2.6.
+We provide a docker image for UniverSC version 1.2.7.
 
 You can import it if you have docker installed.
 

diff --git a/README.html b/README.html
@@ -10,12 +10,12 @@
 src="https://img.shields.io/docker/pulls/tomkellygenetics/universc"
 alt="Docker Pulls" /></p>
 <p><img
-src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.6"
+src="https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.7"
 alt="Docker Image Version (tag latest semver)" /> <img
-src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%[email protected].6%22"
+src="https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label=%[email protected].7%22"
 alt="MicroBadger Layers (latest)" /> <img
-src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.6?label=%22image%[email protected].6"
-alt="Docker Image Size (v1.2.6)" /> <img
+src="https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.7?label=%22image%[email protected].7"
+alt="Docker Image Size (v1.2.7)" /> <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"
@@ -64,9 +64,9 @@
 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/1.2.6/total"
+src="https://img.shields.io/github/downloads/minoda-lab/universc/1.2.7/total"
 alt="GitHub release (latest by date)" /> <img
-src="https://img.shields.io/github/downloads/minoda-lab/universc/1.2.6/total"
+src="https://img.shields.io/github/downloads/minoda-lab/universc/1.2.7/total"
 alt="GitHub release (by tag)" /></p>
 <p><img
 src="https://github.com/minoda-lab/universc/workflows/CI%20to%20Docker%20hub/badge.svg"
@@ -105,7 +105,7 @@ <h1 id="universc">UniverSC</h1>
 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 1.2.6</p>
+<p>UniverSC version 1.2.7</p>
 <p><strong>Maintainers</strong></p>
 <p>Tom Kelly<sup>†</sup> (RIKEN IMS) and Kai Battenberg<sup>†</sup>
 (RIKEN CSRS/IMS)</p>
@@ -453,15 +453,15 @@ <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 1.2.6},
+        note = {https://github.com/minoda-lab/universc package version 1.2.7},
         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">https://doi.org/10.1101/2021.01.19.427209</a>
-package version 1.2.6. <a
+package version 1.2.7. <a
 href="https://github.com/minoda-lab/universc">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},
@@ -473,7 +473,7 @@ <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 1.2.6},
+        note = {package version 1.2.7},
         URL = {https://github.com/minoda-lab/universc},
 }
 </code></pre>
@@ -482,7 +482,7 @@ <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 1.2.6},
+    note = {package version 1.2.7},
     url = {https://github.com/minoda-lab/universc},
   }</code></pre>
 <h3 id="bug-reports">Bug Reports <span id="Issues"><span></h3>
@@ -794,7 +794,7 @@ <h3 id="docker-image">Docker image <span id="Docker"><span></h3>
 administrator.</p>
 <h4 id="pulling-from-remote-dockerhub-repository">Pulling from remote
 DockerHub repository</h4>
-<p>We provide a docker image for UniverSC version 1.2.6.</p>
+<p>We provide a docker image for UniverSC version 1.2.7.</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

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@ affiliations:
    index: 1
  - name: "RIKEN Center for Sustainable Resource Sciences, Suehiro-cho-1-7-22, Tsurumi Ward, Yokohama, Kanagawa 230-0045, Japan"
    index: 2
-date: "Thursday 25 May 2023"
+date: "Tuesday 06 February 2024"
 output:
   prettydoc::html_pretty:
        theme: cayman
@@ -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/1.2.6)
-![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].6")
-![Docker Image Size (v1.2.6)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.6?label="image%[email protected].6)
+![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.7)
+![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].7")
+![Docker Image Size (v1.2.7)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.7?label="image%[email protected].7)
 ![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/1.2.6/total)
-![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.6/total)
+![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.7/total)
+![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.7/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 1.2.6
+UniverSC version 1.2.7
 
 **Maintainers**
 
@@ -242,7 +242,7 @@ default settings, see the [installation](#Uninstalling) or [troubleshooting](#De
     -  STRT-Seq-2i (13 bp barcode, 6 bp UMI): strt-seq-2i
     -  STRT-Seq-2018 (8 bp barcode, 8 bp UMI): strt-seq-2018
 -  SureCell (18 bp barcode, 8 bp UMI): surecell, ddseq, biorad
--  VASA-Seq                          
+-  VASA-Seq
     -  VASA-plate (6 bp UMI, 6 bp barcode): vasa-plate
     -  VASA-drop (6 bp UMI, 16 bp barcode): vasa-drop
 
@@ -391,7 +391,7 @@ 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 1.2.6},
+        note = {https://github.com/minoda-lab/universc package version 1.2.7},
         URL = {https://doi.org/10.1038/s41467-022-34681-z}
 }
 ```
@@ -401,7 +401,7 @@ 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 1.2.6. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+package version 1.2.7. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
 
 ```
 @article {Kelly2021.01.19.427209,
@@ -414,7 +414,7 @@ package version 1.2.6. [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 1.2.6},
+        note = {package version 1.2.7},
         URL = {https://github.com/minoda-lab/universc},
 }
 
@@ -428,7 +428,7 @@ 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 1.2.6},
+    note = {package version 1.2.7},
     url = {https://github.com/minoda-lab/universc},
   }
 ```
@@ -881,7 +881,7 @@ your systems administrator.
 
 #### Pulling from remote DockerHub repository
 
-We provide a docker image for UniverSC version 1.2.6.
+We provide a docker image for UniverSC version 1.2.7.
 
 You can import it if you have docker installed.
 

diff --git a/docker_build.sh b/docker_build.sh
@@ -1,5 +1,5 @@
-version=1.2.5.2-dev
-old_version=1.2.5.1
+version=1.2.7
+old_version=1.2.6
 sed -i "s/$old_version/$version/g"  *md *html .version man/*sh inst/* *.cff
 sed -i 's/universcversion="$old_version"/universcversion="$version"/g' launch_universc.sh
 R -e "knitr::knit('README.Rmd')"; pandoc -f markdown -t html README.md > README.html

diff --git a/inst/CITATION b/inst/CITATION
@@ -15,7 +15,7 @@ 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 1.2.6},
+        note = {https://github.com/minoda-lab/universc package version 1.2.7},
         URL = {https://doi.org/10.1038/s41467-022-34681-z}
 }
 ```
@@ -25,7 +25,7 @@ The preprint can also be found here:
 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/10.1101/2021.01.19.427209](https://doi.org/10.1101/2021.01.19.427209)
-package version 1.2.6. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+package version 1.2.7. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
 
 ```
 @article {Kelly2021.01.19.427209,
@@ -38,7 +38,7 @@ package version 1.2.6. [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 1.2.6},
+        note = {package version 1.2.7},
         URL = {https://github.com/minoda-lab/universc},
 }
 
@@ -51,7 +51,7 @@ 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 1.2.6},
+    note = {package version 1.2.7},
     url = {https://github.com/minoda-lab/universc},
   }
 ```