kangax

use kangax to create the suffix array lookup database for the reference genome

Commands

clean
Remove all job data, not the Moa job itself, note that this must be implemented by the template.
run
run kangax

Filesets

input_fasta
Fasta input file
output_log

output log file

type: map
source: input_fasta
category: output
optional: {}
pattern: ./*.log.txt
output_sfx

output suffix array lookup

type: map
source: input_fasta
category: output
optional: {}
pattern: ./*.sfx

Parameters

block_seq_len

generated suffix blocks to hold at most this length (MB) concatenated sequences

type: integer
default: 3300
optional: True
color_space

generate for colorspace (SOLiD)

type: boolean
default: False
optional: True
extra_params

any extra parameters

type: string
default: ``
optional: True
help

print this help and exit

type: boolean
default: False
optional: True
reference_species

reference species

type: string
default: ``
optional: False
target_dep

generate target file only if missing or older than any independent source files

type: boolean
default: False
optional: True
version

print version information and exit

type: boolean
default: False
optional: True

miscellaneous

Backend
ruff
Author
Mark Fiers, Yogini Idnani
Creation date
Wed Nov 10 07:56:48 2010
Modification date
unknown