If you have a flaski config file you can extract the parameters file from it with:
nextflow run mpg-age-bioinformatics/nf-flaski-configs -r 1.0.0 --raw </path/to/raw/data> --json </path/to/flaski/config.json --out </path/to/output> -profile local
And then run the workflow with:
bash nextflow-local.sh clone </path/to/output/params.json>
This workflow is based on the following nextflow pipes:
- https://github.com/mpg-age-bioinformatics/nf-fastqc
- https://github.com/mpg-age-bioinformatics/nf-cutadapt
- https://github.com/mpg-age-bioinformatics/nf-mageck
- https://github.com/mpg-age-bioinformatics/nf-bagel
- https://github.com/mpg-age-bioinformatics/nf-drugz
- https://github.com/mpg-age-bioinformatics/nf-acer
- https://github.com/mpg-age-bioinformatics/nf-maude
Once run is complete you will find in the work folder the file software.txt with information on all the respective versions used for your run.