Running spacemake

Main modules

After spacemake in configured with the spacemake config command, and projects/samples are added with the spacemake projects command, spacemake can be run with the spacemake run command. It takes the following parameters:

spacemake run \
    --cores CORES \     # number of cores to be used in total
    --dryrun, -n  \     # invokes a dry snakemake run, printing only commands
    --rerun-incomplete, --ri \
                        # forces snakemake to rerun incompletely generated files
    --keep-going  \     # if a job fails, keep executing independent jobs.
                        # we recommend to always set this when running spacemake
                        # overnight
    --printshellcmds, -p \
                        # print shell commands for each rule, if exist
    --touch, -t   \     # rather than running the rules, just touch each file
    --with_fastqc, -wfqc
                        # Run also fastqc as part of the spacemake run

Downsampling

To run a downsampling (or saturation) analysis, one can use the following command:

spacemake run downsample \
    --project_id_list [PROJECT_ID_LIST ...] \
    --sample_id_list [SAMPLE_ID_LIST ...]

In the project_id_list and sample_id_list arguments one can specify which a list of project_id-s and sample_id-s respectively, for which the downsampling should be run. It is possible to set only one, or both of these arguments. If both are set the downsampling will be run on samples for which the project_id and the sample_id are in both lists (intersection).

Note

In addition to the list arguments specified above, the downsample command also takes the same arguments as the simple spacemake run command.