bowtie_pe¶

Run BOWTIE on an set of input files (query) vs a database index.

Commands¶

db: The (basename of the) bowtie database to use.

type: single

category: prerequisite

optional: False

pattern: ../20.bowtiedb/db
fq_forward_input: Fastq input files - forward
fq_reverse_input: Fastq input files - reverse

type: map

source: fq_forward_input

category: input

optional: True

pattern: */*_2.fq
output: Bam output file

type: map

source: fq_forward_input

category: output

optional: {}

pattern: ./*.bam

extra_params: extra parameters to feed to bowtie

type: string

default: ``

optional: True
input_format: Format of the input files

type: set

default: fastq

optional: True
lots_of_data: Keep unmapped reads, unsorted BAM - takes up a lot of space!

type: boolean

default: False

optional: True
max_insertsize: Maximum allowed insertsize

type: integer

default: 250

optional: True
min_insertsize: Minimum allowed insertsize

type: integer

default: 1

optional: True
orientation: orientation of the reads, allowed values are fr, rf, ff

type: {}

default: fr

optional: True