kangar_pe¶

use kangar to pre process raw fq reads

Commands¶

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

fq_forward_input: fastq input files - forward - containing the 5’ end
fq_reverse_input: fastq input files directory - reverse - containing the 3’ end

type: map

source: fq_forward_input

category: input

optional: True

pattern: */*_2.fq
output_log: output log file

type: map

source: fq_forward_input

category: output

optional: {}

pattern: ./*.log.txt
rds_output: output rds file

type: map

source: fq_forward_input

category: output

optional: True

pattern: ./*.rds

extra_params: any extra parameters

type: string

default: ``

optional: True
help: print this help and exit

type: boolean

default: False

optional: True
mode: processing mode 0 - single end create, 1 - paired end create, 2 - output statistics 3 - dump as fasta

type: integer

default: 0

optional: True
quality: fastq quality scoring- 0 - sanger, 1m - Illumina 1.3+, 2 - Solexa < 1.3, 3 - Ignore quality

type: integer

default: 3

optional: True
reads_num: limit number of reads (or dumps) in each input file to this many, 0 if no limit

type: integer

default: 0

optional: True
rm_duplicates: remove duplicate reads retaining only one

type: boolean

default: False

optional: True
trim3: trim this number of bases from 3’ end of sequence

type: integer

default: 0

optional: True
trim5: trim this number of bases from 5’ end of sequence

type: integer

default: 0

optional: True
version: print version information and exit

type: boolean

default: False

optional: True