Support Arriba for other genomes

[kelly-sovacool]

It only supports hg38 and mm10 by default. We may need to reach out to the Arriba maintainer for help creating these fusion files for other genome annotations.

RENEE/config/genomes/biowulf/hg38_30.json

Lines 20 to 22 in 5fb4d14

	"FUSIONBLACKLIST": "s3://nciccbr/Resources/RNA-seq/arriba/blacklist_hg38_GRCh38_v2.0.0.tsv.gz",
	"FUSIONCYTOBAND": "s3://nciccbr/Resources/RNA-seq/arriba/cytobands_hg38_GRCh38_v2.0.0.tsv",
	"FUSIONPROTDOMAIN": "s3://nciccbr/Resources/RNA-seq/arriba/protein_domains_hg38_GRCh38_v2.0.0.gff3"

[kopardev]

Linked to #12

[kelly-sovacool]

there is likely an if statement checking for the genome and only running arriba on hg38 -- will need to remove this

[kelly-sovacool]

hg19 blacklist and fusion files are included in arriba: https://arriba.readthedocs.io/en/latest/input-files/#blacklist

first let's download on biowulf, later will put them in our s3 bucket

[kelly-sovacool]

there is likely an if statement checking for the genome and only running arriba on hg38 -- will need to remove this

this appears to be implemented correctly

RENEE/workflow/rules/paired-end.smk

Line 612 in ee1a9e4

if references(config, pfamily, ['FUSIONBLACKLIST', 'FUSIONCYTOBAND', 'FUSIONPROTDOMAIN']):

[kelly-sovacool]

closing in favor of #12. All that is needed is to upload the mm39 resources to S3 and update the jsonmaker rule to support mm39

RENEE/workflow/rules/build.smk

Line 657 in 6af726a

rule jsonmaker: