Running a datatest

Running iKISS using the dataset provided by the tool. Here it will downloaded and decompressed on the TEST directory.

ikiss test_install --help
ikiss test_install -d TEST

Launch suggested command line done by iKISS, in local or cluster:

ikiss run --help
ikiss run -c TEST/data_test_config.yaml --apptainer-args "--bind $HOME"
# @IFB
ikiss run -c TEST/data_test_config.yaml --apptainer-args "--bind /shared:/shared"
#you can also use snakemake parameters as
ikiss run -c TEST/data_test_config.yaml --rerun-incomplete --nolock --apptainer-args "--bind $HOME"

Warning

In i-Trop cluster, run iKISS using ONLY a node, data has to be in “/scratch” of chosen node. Use nodelist : nodeX parameter inside of config.yaml file.

• If you are on your local computer, you can pass -t params to parallelize in the local machine.

ikiss run_local --help
ikiss run_local -t 8 -c TEST/data_test_config.yaml --apptainer-args "--bind $HOME"

Note

In local mode, its possible to allocate threads to some rules using –set-threads snakemake argument such as

ikiss run_local -t 8 -c TEST/data_test_config.yaml --set-threads kmers_gwas_per_sample=4 mapping_kmers=2 filter_bam=2 kmer_position_from_bam=4 pcadapt=2 extract_kmers_from_bed=2