Command line options

Under construction

This page is still under construction and will contain more detailed information in the future

stemcnv-check has 3 different subcommands:

• setup-files: Create example files for project setup

• make-staticdata: Create static data for SNP array

• run: Run the analysis workflow

Common command line options for all subcommands are:

-h, --help

Show this help message and exit

--version

Show version information and exit

-v, --verbose

More verbose output and additional logging, maximum verbosity at -vv

-c, --config FILE

Filename of config file. Default: config.yaml Note: if a global config exists in the cache path, it will also be used by default

-s, --sample-table FILE

Filename of sample table, can be tsv or xlsx format (1st sheet is read). Default: sample_table.tsv or sample_table.xlsx

Options specific to the setup-files subcommand are:

--config-details {minimal,medium,advanced,complete}

Level of detail for the config file. Default: minimal

--sampletable-format {tsv,xlsx}

Format of the sample table. Default: tsv

--ovrrwrite

Allow overwriting of existing files

Options specific to the make-staticdata and the run subcommands are:

-d, --directory PATH

Directory to run pipeline in. Default: current directory

-n, --local-cores INT

Number of cores for local submission. Default: 4

--cache-path PATH

Override auto-selection of the cache path to a specific directory. The default cache path is defined in the conifg file.

--no-cache

Do not use a cache directory for workflow created metadata. (cache includes: global array definition config, conda envs, singularity images, and reference data). The default cache path is defined in the conifg file.

--bind-points BIND_POINTS

Additional bind points for apptainer containers, intended for expert users. Use i.e. ‘/path’ to make it available in apptainer, useful in case local directory contains symlinks that won’t resolve in the container.

Options specific to only the run subcommand are:

-t, --target {complete,report,collate-summary,summary-tables,collate-cnv-calls,combined-cnv-calls,PennCNV,CBS,SNP-data,gtc-data}

Final target of the pipeline. Default: complete

--collate-date [COLLATE_DATE]

Add a date to the collate output files. Default without argument: today’s date

--snakemake-help

Show snakemake help message, all snakemake options must be passed after ‘–’