This pipeline takes a runfolder and runs ngs2counts on it creating count files which are saved in the incoming folder on Miarka.
nextflow run main.nf --input_folder <path_to_runfolder> --ngs2counts_executable <path_to_ngs2counts_version>
When running on Uppmax, use -profile uppmax
--input_folder <path_to_runfolder>: path to the runfolder for which ngs2counts needs to be run--ngs2counts_executable <path_to_ngs2counts_version>: path to ngs2counts version to use--ngs2counts_extra_args <string_with_extra_args>: optional parameter for extra ngs2counts arguments
The pipeline will write the results in the input_folder. Creating the following structure:
input_folder
├── ngs2counts
│ ├── counts_*.csv
│ └── run_metadata.json
├── ngs2counts_log.txt
└── ngs2counts_version.txt
nf-test test