hagfish

Run hagfish_extract & hagfish_combine

Run the preparatory steps for hagfish

Commands

clean

remove all Hagfish files

finish

finish up - find gaps - combine plots - create a report

run

Run hagfish

Filesets

fasta

fasta sequence of the reference

type: single

category: prerequisite

optional: False

pattern: {}

input

“hagfish” input files

output

“hagfish” touch files - track what files are done - please do not touch this!

type: map

source: input

category: output

optional: True

pattern: ./touch/*.touch

Parameters

circosbinsize

Binsize for generating circos formatted histograms

type: int

default: {}

optional: True

max_ok

Maximal acceptable insert size for an aligned pair. If omitted, hagfish will make an estimate

type: int

default: 0

optional: True

min_ok

Minimal acceptable insert size for an aligned pair. If omitted, hagfish will make an estimate

type: int

default: 0

optional: True

miscellaneous

Backend

ruff

Author

Mark Fiers

Creation date

Tue Mar 29 16:34:19 2011

Modification date

Thu, 19 May 2011 20:49:04 +1200