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.