All the parameters except modules are mandatory.
| Parameter | Description | Required by |
|---|---|---|
genome_version |
the genome version of the organism in which the experiment has been done (36 or 38 most of time). This parameter is required to build the path of the STAR genome index |
STAR |
genome_release |
the genome release of the organism in which the experiment has been done (86 or 89 most of time). This parameter is required to build the path of the STAR genome index |
STAR |
design |
the path of the csv design file |
every processes because the sample column values will be used to name the output files, the experimental condition columns values will be used by DESeq2 |
strandedness |
the strandedness of the reads (none, forward, reverse), but the pipeline determines this by itself anyway |
STAR |
conda |
the absolute path to the conda environment | STAR |
modules |
the modules you want to use if you want a different version for the default |
There are two ways to specify the analysis parameters : with a parameter yml file or via command line arguments (see Running the pipeline).