Snakemake parameters

NEEDS edit Found in file: scripts/snakemake/snakemake_config.yaml

These parameters are either set in the GUI, or if you’re running DICAST via cli, these parameters determine properties your DICAST run.

Possible_overwrite_acknowledge:

When running DICAST first, an output directory is created. When your run is finished, please rename the output directory, if you want to save this output; so that you don’t overwrite outputs with the second run of DICAST.

ASimulatoR files such as src/ASimulatoR/out/event_annotation.tsv are also overwritten between runs, if ASimulatoR is run again.

true or false

true: DICAST runs uninterrupted.

false: DICAST run is interrupted until true

ASimulatoR:

do: True / False

Run ASimulatoR with the configs as stored in file: :scripts/snakemake/snakemake_config

( See ASimulatoR config)

Mapping_tools:

What_tools_to_run: ‘<insert name of mapping tools to run, separated by spaces>’

pick one of the following bbmap contextmap crac dart gsnap hisat mapsplice minimap segemehl star subjunc

Example: to run all tools: ‘bbmap contextmap crac dart gsnap hisat mapsplice minimap segemehl star subjunc’

Example: to some two tools: ‘minimap star’

Example: to run one tool: ‘star’

Alternative_splicing_detection_tools:

What_tools_to_run: ‘<insert name of Alternative Splicing tools to run, separated by spaces>’

pick one of the following asgal aspli eventpointer irfinder majiq sgseq spladder whippet

Example: to run all tools: ‘asgal aspli eventpointer irfinder majiq sgseq spladder whippet’

Example: to some two tools: ‘eventpointer whippet’

Example: to run one tool: ‘whippet’