about Configuration file (bulk-config.json)

[ajcorriaosorio]

Hi,

I would like to know what to put here to replace yours, this is not very clear in the README, thanks :

"spike_in_bt2idx": "/gcdata/gcproj/fulong/Data/Genomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index",

"spike_in_sequence": "/gcdata/gcproj/fulong/Data/Genomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa",

Do I need to download these ones too?

"picardjarfile": "picard-2.8.0.jar",
"trimmomaticjarfile": "trimmomatic-0.36.jar",
"makecutmatrixbin": "/homes6/fulong/.local/bin"

thanks