update documentation for 1.2.3

.version

@@ -1 +1 @@
-1.2.2
+1.2.3

CHANGELOG

@@ -1,3 +1,15 @@
+### 1.2.3
+
+- enables GitHub citation widget
+
+- updates SmartSeq2 and SmartSeq3 default barcodes 
+
+- updates SmartSeq2 adapter sequences and documents chemistry configurations
+
+- enables running Slurm scheduler with automatic template configuration
+
+- correctly sets the source directory to call subroutines and whitelists on Slurm (https://stackoverflow.com/questions/56962129/how-to-get-original-location-of-script-used-for-slurm-job)
+
 ### 1.2.2
 
 - bug fixes for detecting I1 and I2 files

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/1.2.2)
-![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].2")
-![Docker Image Size (v1.2.2)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.2?label="image%[email protected].2)
+![Docker Image Version (tag latest semver)](https://img.shields.io/docker/v/tomkellygenetics/universc/1.2.3)
+![MicroBadger Layers (latest)](https://img.shields.io/microbadger/layers/tomkellygenetics/universc/latest?label="[email protected].3")
+![Docker Image Size (v1.2.3)](https://img.shields.io/docker/image-size/tomkellygenetics/universc/1.2.3?label="image%[email protected].3)
 ![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/1.2.2/total)
-![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.2/total)
+![GitHub release (latest by date)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.3/total)
+![GitHub release (by tag)](https://img.shields.io/github/downloads/minoda-lab/universc/1.2.3/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 1.2.2
+UniverSC version 1.2.3
 
 **Maintainers**
 
@@ -353,21 +353,21 @@ 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/10.11.2.2021.01.19.427209](https://doi.org/10.11.2.2021.01.19.427209)
-package version 1.2.2. [https://github.com/minoda-lab/universc](https://github.com/minoda-lab/universc)
+bioRxiv 2021.01.19.427209; doi: [https://doi.org/10.11.2.3021.01.19.427209](https://doi.org/10.11.2.3021.01.19.427209)
+package version 1.2.3. [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 = {10.11.2.2021.01.19.427209},
+        doi = {10.11.2.3021.01.19.427209},
         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 1.2.2},
+        note = {package version 1.2.3},
         URL = {https://github.com/minoda-lab/universc},
 }
 
@@ -378,7 +378,7 @@ package version 1.2.2. [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 1.2.2},
+    note = {package version 1.2.3},
     url = {https://github.com/minoda-lab/universc},
   }
 ```
@@ -831,7 +831,7 @@ your systems administrator.
 
 #### Pulling from remote DockerHub repository
 
-We provide a docker image for UniverSC version 1.2.2.
+We provide a docker image for UniverSC version 1.2.3.
 
 You can import it if you have docker installed.
 
@@ -939,14 +939,14 @@ cellrangerpath=`which cellranger`
 if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
     rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA
 fi
-if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.2/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.2/star/SA ]]; then
-    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.2/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.2/star/SA
+if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.3/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.3/star/SA ]]; then
+    rsync $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.3/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.3/star/SA
 fi
 ```
 
 This creates a reference for Cell Ranger here:
 
-- test/cellranger_reference/cellranger-tiny-ref/1.2.2
+- test/cellranger_reference/cellranger-tiny-ref/1.2.3
 
 - test/cellranger_reference/cellranger-tiny-ref/3.0.0
 
@@ -985,7 +985,7 @@ gffread test/cellranger_reference/cellranger-tiny-ref/genes-1.2.0.gff3 -T -o tes
 To generate new references we first remove the references imported.
 
 ```
-rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.2 test/cellranger_reference/cellranger-tiny-ref/3.0.0
+rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.3 test/cellranger_reference/cellranger-tiny-ref/3.0.0
 ```
 
 We then generate references from the FASTA and GTF files as shown in the following examples:
@@ -1241,26 +1241,26 @@ bash /universc/launch_universc.sh --id "test-10x-v3" --technology "10x" \
 Obtain DropSeq data from public database:
 
 ```
-wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1.2.292\&format\=file\&file\=GSM1.2.292%5FPure%5FHumanMouse%2Ebam
-mv index.html\?acc=GSM1.2.292\&format=file\&file=GSM1.2.292%5FPure%5FHumanMouse%2Ebam GSM1.2.29.bam
-samtools sort -n GSM1.2.29.bam > GSM1.2.29.qsort
-samtools view  GSM1.2.29.qsort  HUMAN_21:9825832-48085036 > GSM1.2.29.qsort2
-samtools sort -O BAM GSM1.2.29.bam > GSM1.2.29.sort.bam
-samtools index GSM1.2.29.sort.bam
-samtools view  GSM1.2.29.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.29.chr21.bam
-samtools view -O BAM  GSM1.2.29.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.29.chr21.sort.bam
-samtools sort -n GSM1.2.29.chr21.sort.bam -o GSM1.2.29.chr21.qsort.bam
-bedtools bamtofastq -i GSM1.2.29.chr21.qsort.bam -fq GSM1.2.292_chr21_R1.fastq
-mv GSM1.2.292_chr21_R1.fastq GSM1.2.292_chr21_R2.fastq
+wget https://www.ncbi.nlm.nih.gov/geo/download/\?acc\=GSM1.2.392\&format\=file\&file\=GSM1.2.392%5FPure%5FHumanMouse%2Ebam
+mv index.html\?acc=GSM1.2.392\&format=file\&file=GSM1.2.392%5FPure%5FHumanMouse%2Ebam GSM1.2.39.bam
+samtools sort -n GSM1.2.39.bam > GSM1.2.39.qsort
+samtools view  GSM1.2.39.qsort  HUMAN_21:9825832-48085036 > GSM1.2.39.qsort2
+samtools sort -O BAM GSM1.2.39.bam > GSM1.2.39.sort.bam
+samtools index GSM1.2.39.sort.bam
+samtools view  GSM1.2.39.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.39.chr21.bam
+samtools view -O BAM  GSM1.2.39.sort.bam  HUMAN_21:9825832-48085036 > GSM1.2.39.chr21.sort.bam
+samtools sort -n GSM1.2.39.chr21.sort.bam -o GSM1.2.39.chr21.qsort.bam
+bedtools bamtofastq -i GSM1.2.39.chr21.qsort.bam -fq GSM1.2.392_chr21_R1.fastq
+mv GSM1.2.392_chr21_R1.fastq GSM1.2.392_chr21_R2.fastq
 fastq-dump -F --split-files SRR1873277
-fastq_pair GSM1.2.292_chr21_R2.fastq SRR1873277_1.fastq
+fastq_pair GSM1.2.392_chr21_R2.fastq SRR1873277_1.fastq
 head -n 117060 SRR1873277_1.fastq.paired.fq 117060 > SRR1873277_1.fastq.paired.fq
-head -n 117060 GSM1.2.292_chr21_R2.fastq.paired.fq > GSM1.2.292_chr21_R2.fastq.paired.fq
-cp SRR1873277_1.fastq.paired.fq  GSM1.2.292_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test
-cp SRR1873277_1.fastq.paired.fq  GSM1.2.292_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test
+head -n 117060 GSM1.2.392_chr21_R2.fastq.paired.fq > GSM1.2.392_chr21_R2.fastq.paired.fq
+cp SRR1873277_1.fastq.paired.fq  GSM1.2.392_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test
+cp SRR1873277_1.fastq.paired.fq  GSM1.2.392_chr21_R2.fastq.paired.fq ~/repos/universc/test/shared/dropseq-test
 mv SRR1873277_1.fastq.paired.fq SRR1873277_R1.fastq
-mv GSM1.2.292_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq
-mv GSM1.2.292_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq
+mv GSM1.2.392_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq
+mv GSM1.2.392_chr21_R2.fastq.paired.fq  universc/test/shared/dropseq-test/SRR1873277_R2.fastq
 ```
 
 Run UniverSC: