A Nextflow pipeline for pang genome analyses including phylogenic tree. The pipeline is a upgraded version of the pipeline fl_cg_snp.
Nextflow should be installed. The detail of installation can be found in https://github.com/nextflow-io/nextflow.
Python3 is needed.
Singularity is also needed. The detail of installation can be found in https://singularity-tutorial.github.io/01-installation/.
- put your gff files into directory /gffs. Test data can be found in the directory /gffs/testdata. If you want to use the test data, copy them to the directory /gffs.
- open file "parames.yaml", set the parameters.
- get into the top of the pipeline directory, run "sbatch sbatch_fl_cg_snp_nf.sh"
All results can be found in the directory /output.