Expects a config containing the following: - GENOME_FASTA - HOST_GTF
Yields the following results/masked_genome_plus_tes/genome.masked.fasta results/masked_genome_plus_tes/transcripts_and_tes.gtf
Must include all configuration for any modules as well.
It has a default repeatmasker argument set, which can be overridden by editing the following portion of the config: REPEATMASKER_ARGS
Previous versions of this workflow only pulled TE seqs from DFAM. In the current version, you can optionally include a REPEAT_FASTA entry in the configfile.
Detection of this entry skips the DFAM extraction step and allows you to use any fasta as an argument to the -lib param for repeatmasker. It is currently set
to a curated Dmel TE set made available at the Bergman Lab github repo.