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: mapsource: input_fastacategory: outputoptional: {}pattern: ./*.log.txt- output_sfx
output suffix array lookup
type: mapsource: input_fastacategory: outputoptional: {}pattern: ./*.sfx
Parameters¶
- block_seq_len
generated suffix blocks to hold at most this length (MB) concatenated sequences
type: integerdefault: 3300optional: True- color_space
generate for colorspace (SOLiD)
type: booleandefault: Falseoptional: True- extra_params
any extra parameters
type: stringdefault: ``optional: True- help
print this help and exit
type: booleandefault: Falseoptional: True- reference_species
reference species
type: stringdefault: ``optional: False- target_dep
generate target file only if missing or older than any independent source files
type: booleandefault: Falseoptional: True- version
print version information and exit
type: booleandefault: Falseoptional: True
miscellaneous¶
- Backend
- ruff
- Author
- Mark Fiers, Yogini Idnani
- Creation date
- Wed Nov 10 07:56:48 2010
- Modification date
- unknown