GitLab

Fusioncatcher crashes if the maximum number of junction reads is
exceeded. This commit adds a parameter to the fusioncatcher rule to
make this configurable, and also increases the default limit from 100000
to 150000.

Rattle is an extension to snakemake which makes it easier to work with
settings and output files. It was developed to work around some of the
limitations in earliers versions of Snakemake. Now that Snakemake has
matured, Rattle does not provide any benefit over vanilla Snakemake.

Switch to version 1.00 of fusioncatcher, which is available from conda
like most other tools. Remove the fusioncatcher_exe entry from
config-base.yml, and update the Snakefile to use fusioncatcher from
conda.

As a side effect, all optional parts of the pipeline which depend on the
availability can now be executed by default.

README.md has been updated to reflect these changes

Apparently the target file may be removed if we do a rerun
on an existing directory.