bwa_samse

Generate alignments in SAM format given single end reads, using both ‘bwa samse’.

Commands

clean

Remove all job data, not the Moa job itself

run

run bwa samse

Filesets

fq_input

fastq input file

output_bam

output bam file

type: map

source: fq_input

category: output

optional: {}

pattern: ./*.bam

sai_input

sai input directory - filenames must correspond to the fastq input files

type: map

source: fq_input

category: input

optional: False

pattern: */*.sai

Parameters

db

bwa database to align against

type: string

default: ``

optional: False

max_aln_out

Maximum number of alignments to output in the XA tag for reads paired properly

type: integer

default: 3

optional: True

miscellaneous

Backend

ruff

Author

Yogini Idnani, Mark Fiers

Creation date

Wed Nov 25 17:06:48 2010

Modification date

unknown