StarScope provides a convenient way to run ThunderBio single cell analysis nextflow pipelines. scRNA-seq workflow uses starsolo (https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md) and Seurat package (https://satijalab.org/seurat/) as the core modules to process 3' single cell RNA-seq data and generate a concise HTML report. We also integrated single cell immune repertopire and ATAC analysis workflows as other two subcommands, both of which were also built using nextflow.

ThunderBio will provide human and mouse pre-built reference and two sets example data upon request. The demo_data fold contains two directories, human and mouse. In each directory, user could invoke the pipeline by running command below. Please note the reference index has to be placed in the same parent folder of the demo_data.

## Human Data Testing with conda or docker
cd demo_data/human
starscope run --input sampleList.csv --config thunderbio_human_conda.config
starscope run --input sampleList.csv --config thunderbio_human_docker.config

## Mouse Data Testing with conda or docekr
cd demo_data/mouse

demo_data/
├── human
│   ├── human_test.R1.fq.gz
│   ├── human_test.R2.fq.gz
│   ├── sampleList.csv
│   ├── thunderbio_human_conda.config
│   └── thunderbio_human_docker.config
├── mouse
│   ├── mouse_test.R1.fq.gz
│   ├── mouse_test.R2.fq.gz
│   ├── sampleList.csv
│   ├── thunderbio_mouse_conda.config
│   └── thunderbio_mouse_docker.config
└── V2_barcode_seq_210407_concat.txt

• Updated script for saturation calculation, and included UMI and gene hist data for {preseqR} prediction

• Now a tsv summary file will be outputted in the report process

• Added --outBAMsortingBinsN 300 option to STARsolo process to solve the RAM issue when sorting a very large BAM file, refer to STAR #870

• Use soft link instead of cat when there is only one fastq file

• Added support for VDJ subworkflow to only analyze BCR or TCR dataset

• Added support for publishing saturation json file

• Honer the memory option in the report process

• Added option for publishing starsolo BAM output

• Added option to enable conda env for nextflow 22.10, and the nextflow version was fixed to 22.04

• Added VDJ workflow (GEX+VDJ)

• Removed time limit for process resources

• Modified the margin of the tables in the 3'-scRNA-Seq report

• Adjusted knee plot to fixed size and center positioned

• Added pipeline running information to the reports

• Fixed issue for saturation calculation script when there is no whitelist provided

• Output a full list of DEGs

• Updated STAR to v2.7.10a in both the docker image and the conda environment

• Adapt the pipeline to generate report for starsolo --soloMultiMappers option, only "Unique" and "EM" are supported by now.

• Changed the default parameter for --soloFeatures to "GeneFull", which includes both exon and intron reads

• Fixed the issue that RunPCA uses up all cores and consumes too much memory (Seurat #3991)

• Changed h5file format to H5Seurat

• Disabled sass cache in rmd report

• Changed future package strategy to multisession to avoid fork errors

• Raw gene/barcode count table will be stored in a loom file and published for subsequent analysis

• Mapping metrics will be written to a json file

• Added support for 5' RNA-seq library

• Now the BAM output will not by published

• Added support for counting intron reads

• Added check_version command, to print all software versions including docker or conda engine information

• Fixed STAR to 2.7.9a and samtools to 1.15

• Fixed issue that no report generated if too few cells detected

• Fixed issue that no report generated if there are too few cells left after filtering by nFeature >= 200

• Set thunderbio data running parameters as defaults instead of 10x parameters

• Added whitelists for thunderbio V2, 10x V2 and V3

• Fixed nextflow default path issue

• Fixed conda env name issue

• Implemented docker container running environment

• Added a new script for user to generate 10x compatible STAR reference

• Implemented mkref command

• Added output section for README

• Implemented run command

• Added running env checking procedure