recursive_map

Recursively map a genome to the reference

Recursively map a resequence dataset against a reference genome

Commands

run
recusive map

Filesets

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
output

base output filename

type: single
category: output
optional: True
pattern: output

reference

type: single
category: prerequisite
optional: False
pattern: */*

Parameters

iterations

no of iterations to run

type: integer
default: 3
optional: True
param_first

First set of parameters - get the low hanging fruit

type: string
default: –fast
optional: True
param_second

Second set of parameters - more sensitive

type: string
default: –very-sensitive
optional: True
threads

Number of threads to use

type: integer
default: 4
optional: True

miscellaneous

Backend
ruff
Author
Mark Fiers
Creation date
Fri, 08 Jun 2012 13:32:30 +1200
Modification date
Fri, 08 Jun 2012 13:43:19 +1200