A Nextflow pipeline based on an existing tutorial by Praneet Chaturvedi and Abhijit Badve.
There's no need to download this repository, it can be downloaded and run directly from the command line as such:
nextflow run slagtermaarten/bulk_velo-nf
--bam_dir /path/to/dir/containing/bam_files
--bam_glob '*.bam'
--cpu 8
--outdir 'results'
--chroms '1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X Y'
--mask /path/to/intron_location_mask
--gtf /path/to/gene_locations
--N_pc 10
The parameter names should mostly be self-explanatory. bam_glob allows you to sub-select
bam files in the bam_dir using regex. N_pc sets the number of principal components on
which scVelo is run.
Of course, the intron masking file and gtf files should be compatible with the reference genome to which the RNASeq data was aligned. For more information, please see the original tutorial on which this was based.