Nextflow Pipeline for the QC, Filtering and Creation of .arrow Files...
Installation
This package can be installed from Github using the remotes package.
You may first need to register your GitHub PAT, as this is a private repository.
Sys.setenv(GITHUB_PAT = "your-access-token-here")
remotes::install_github("bwh-bioinformatics-hub/scATAC_Seq_Pipeline")
wget -qO- https://get.nextflow.io | bash
Make the binary executable on your system by running
chmod +x nextflow
The only column that is a requirement to run the nextflow pipeline is the "Sample" column.