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Input JSON

An input JSON file includes all genomic data files, parameters and metadata for running pipelines. Our pipeline will use default values if they are not defined in an input JSON file.

We provide two example JSON files including single-species and mixed-species.

Pipeline parameters

Parameter Type Description
main.ID String MANDATORY. Sample id.
main.fastq1 Fastq MANDATORY. Read 1 in fastq format. Can be gzipped. Fastqs from different lanes can be seperated with comma. For example, "L01_read_1.fq.gz,L02_read_1.fq.gz,..."
main.fastq2 Fastq MANDATORY. Read 2 in fastq format. Can be gzipped. Fastqs from different lanes can be seperated with comma. For example, "L01_read_2.fq.gz,L02_read_2.fq.gz,..."
main.outdir Directory MANDATORY. Output directory
main.root Directory MANDATORY. Directory of this pipeline.
main.expectCell Integer Optional, default: 0. Expected cell number.
main.forceCell Integer Optional, default: 0. Specified number of cells.
main.umiCount Integer Optional, default: 0. Threshold of barcode's umi, anything above that would be defined as contribution from vaid cells.
main.umilow Integer Optional, default: 50. Expected UMIs count per cell threshold.
main.config JSON file MANDATORY. Read structure configure. UMI and Cell Barcode specified in this file. Can be found at config/ directory.
main.Rscript Path MANDATORY. Path to Rscript.
main.Python3 Path MANDATORY. Path to Python3.
main.refdir Directory MANDATORY. STAR index directory of genome reference.
main.gtf File Path MANDATORY. gtf file of genome reference.
main.chrom File Path Optional, default: config/species_binding.txt directory. Chromosome and species correspondence files in the mixed species process. And Single species process don't need this file.
main.species String Optional, default: Null. Species.
main.original String Optional, default: Null. original.
main.SampleTime String Optional, default: Null. Sample time.
main.ExperimentalTime String Optional, default: Null. Experimental time.