update documentation for 1.2.0

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

1.1.7

1.2.0

### 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)

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"

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,

        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},

}

    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},

  }

```