Conda environments defined under environment/conda, the Snakemake base environment is defined in the file conda_smkenv.yml.

Run pipeline as follows:

snakemake -n -d ../run_folder/ --cluster-status ../run_folder/hhu_hilbert.py --configfiles smk_config/smk_cfg_env-hhu.yml smk_config/kmervar_cfg.yml --profile environment/snakemake/cluster/hhu_pbs master

Configuration file kmvar_cfg.yml contains path to assemblies and k-mer size.

Current project folder:

/gpfs/project/projects/medbioinf/projects/kmvar

Input assemblies:

/gpfs/project/projects/medbioinf/projects/kmvar/assemblies

Adding more assemblies (FASTA format) to the above folder and (force) rerunning the pipeline will trigger an update for the k-mer counting.

The main output file of shared unique k-mers is located under:

run_folder/output/shared_kmers/uniq.k31.txt.gz