autohagfish¶
Automatically run bowtie & hagfish combined
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: singlecategory: prerequisiteoptional: Falsepattern: {}- fw_fq
- forward fq input
- outbase
basename for output files
type: mapsource: fw_fqcategory: outputoptional: Truepattern: ./*- rev_fq
reverse fq input
type: mapsource: fw_fqcategory: inputoptional: Truepattern: */*2.fq
Parameters¶
- max_ok
Maximal acceptable insert size for an aligned pair. If omitted, hagfish will make an estimate
type: intdefault: 0optional: True- min_ok
Minimal acceptable insert size for an aligned pair. If omitted, hagfish will make an estimate
type: intdefault: 0optional: True- threads
no threads to use
type: integerdefault: 8optional: 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