Nextflow wrapper to execute XenoCell, a tool to separate graft from host reads in single-cell RNA-seq xenograft experiments (https://gitlab.com/XenoCell/XenoCell, https://doi.org/10.1186/s12920-021-00872). Not affiliated with the original authors of XenoCell.
Currently supports up to two lanes per fastq file. An example Nextflow config file is included, which will need to be modifed to suit any particular system. Currrently runs XenoCell from an automatically pulled docker container via Singularity.
Command line options:
--index: Combined Xenome reference genome index [currently needs to be pre-generated before running the workflow]
--outdir: Desired output directory
Method parameters (see documentation of the original tool):
--barcode_start: [Default: 1]
--barcode_length: = [Default: 16]
--lower_threshold_host: = [Default: 0.9]
--upper_threshold_graft: = [Default: 0.1]
--threads = [Default: 16]
--memory = [Default: 60]
--compression_level = [Default: 1]
Any other method parameters may be changed from defaults by modifying the code of xenocell.nf.
--fastqdir: The base directory storing sample fastq files.
Currently expects the latter to be contained within subdirectories named after each sample within this base directory. Reads are expected to be named in a way that ends with a pattern like "_L001_R1_001.fastq.gz". To change the latter, modify the parameters below with any alternative pattern:
--fastq_lane_1_read_1: [Default: "${params.fastqdir}/*/*_L001_R1_001.fastq.gz"]
--fastq_lane_1_read_2: [Default: "${params.fastqdir}/*/*_L001_R2_001.fastq.gz"]
--fastq_lane_2_read_1: [Default: "${params.fastqdir}/*/*_L002_R1_001.fastq.gz"]
--fastq_lane_2_read_2: [Default: "${params.fastqdir}/*/*_L002_R2_001.fastq.gz"]