update documentation for 1.2.0

minoda-lab · Jan 26, 2022 · b43454c · b43454c
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diff --git a/.gitattributes b/.gitattributes
@@ -72,3 +72,11 @@ test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R1_001.fastq.gz filter=l
 test/shared/cellranger-tiny-fastq/3.0.0/tinygex_S1_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
 whitelists/KAPA_UDI_Index2_i5.txt filter=lfs diff=lfs merge=lfs -text
 whitelists/KAPA_UDI_Index1_i7.txt filter=lfs diff=lfs merge=lfs -text
+test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+test/shared/smartseq3-test/test-smartseq-hek293t_S2_L002_I1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+test/shared/smartseq3-test/test-smartseq-hek293t_S2_L002_I2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+test/shared/smartseq3-test/test-smartseq-hek293t_S2_L002_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+test/shared/smartseq3-test/test-smartseq-hek293t_S2_L002_R2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
+test/shared/smartseq3-test/test-smartseq-hek293t_S2_L001_I2_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
diff --git a/.version b/.version
@@ -1 +1 @@
-1.1.7
+1.2.0
diff --git a/CHANGELOG b/CHANGELOG
@@ -1,3 +1,13 @@
+### 1.2.0
+
+- backend to fully functional GUI app
+
+- updates to support 10x 3` scRNA version 1
+
+- updates test jobs and test data for SmartSeq3
+
+- automated file detection for R3 and R4 read files
+
 ### 1.1.7
 
 - uses reverse complement barcode whitelist for inDrops v1 and v2 (automatically generated)

diff --git a/docker_build.sh b/docker_build.sh
@@ -1,5 +1,5 @@
-version=1.1.7
-old_version=1.1.6.2
+version=1.2.0
+old_version=1.1.7
 sed -i "s/$old_version/$version/g"  *md *html launch_universc.sh .version man/*sh inst/*
 R -e "knitr::knit('README.Rmd')"; pandoc -f markdown -t html README.md > README.html
 echo "updating GitHub version $version"

diff --git a/inst/CITATION b/inst/CITATION
@@ -6,21 +6,21 @@ 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/10.11.1.7021.01.19.427209](https://doi.org/10.11.1.7021.01.19.427209)
-package version 1.1.7. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.11.2.0021.01.19.427209](https://doi.org/10.11.2.0021.01.19.427209)
+package version 1.2.0. [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 = {10.11.1.7021.01.19.427209},
+        doi = {10.11.2.0021.01.19.427209},
         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 1.1.7},
+        note = {package version 1.2.0},
         URL = {https://github.com/minoda-lab/universc},
 }
 
@@ -31,7 +31,7 @@ package version 1.1.7. [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 1.1.7},
+    note = {package version 1.2.0},
     url = {https://github.com/minoda-lab/universc},
   }
 ```
diff --git a/podman_build.sh b/podman_build.sh
@@ -1,5 +1,5 @@
-version=1.1.7
-old_version=1.1.6.2
+version=1.2.0
+old_version=1.1.7
 sed -i "s/$old_version/$version/g"  *md *html  launch_universc.sh .version man/*sh inst/*
 R -e "knitr::knit('README.Rmd')"; pandoc -f markdown -t html README.md > README.html
 echo "updating GitHub version $version"