soapdenovo_postprocess¶

Run Soapdenovo

Commands¶

fq_forward: fastq input files directory - forward
fq_reverse: fastq input files directory - reverse

type: map

source: fq_forward

category: input

optional: True

pattern: */*_2.fq
input: input scaffold to process

type: single

category: input

optional: False

pattern: {}
output: output file to generate

type: single

category: output

optional: True

pattern: final.fasta

avg_insert: library insert size

type: integer

default: 200

optional: {}
noruns: no times to run gapcloser & SSPace

type: integer

default: 2

optional: True
run_sspace: run SSPace? use

type: boolean

default: True

optional: True
sspace_executable: SSPace executable

type: {}

default: SSPACE_Basic_v2.0.pl

optional: True
sspace_extra_variables: Extra variables to pass to Sspace

type: {}

default: ``

optional: True
threads: no threads to use

type: integer

default: 8

optional: True