smalt_pe¶

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

Commands¶

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

type: single

category: prerequisite

optional: False

pattern: ../10.smaltdb/db
fasta: reference fasta file

type: single

category: prerequisite

optional: False

pattern: *.fasta
fq_forward_input: fastq input files directory - forward
fq_reverse_input: fastq input files directory - reverse

type: map

source: fq_forward_input

category: input

optional: True

pattern: */*_2.fq
output: output BAM file (automatically converted & filtered for reads that to not map)

type: map

source: fq_forward_input

category: output

optional: {}

pattern: ./*.sam

extra_params: extra parameters to feed to smalt

type: string

default: ``

optional: True
max_insertsize: Maximum allowed insertsize

type: integer

default: 250

optional: True
min_insertsize: Minimum allowed insertsize

type: integer

default: 1

optional: True
output_format: output format (sam or samsoft)

type: {}

default: sam

optional: True
pairtype: pair type (pe: fr/illumina short; mp: rf/illumina mate pairs or pp: ff

type: {}

default: pe

optional: True
threads: No threads to use

type: int

default: 4

optional: True