smalt_pe¶
Run SMALT on an set of input files (query) vs a database index.
Commands¶
- clean
- Remove all job data, not the Moa job itself
- run
- Execute SMALT with with paired-end fastq
Filesets¶
- db
The (basename of the) smalt database to use.
type: singlecategory: prerequisiteoptional: Falsepattern: ../10.smaltdb/db- fasta
reference fasta file
type: singlecategory: prerequisiteoptional: Falsepattern: *.fasta- fq_forward_input
- fastq input files directory - forward
- fq_reverse_input
fastq input files directory - reverse
type: mapsource: fq_forward_inputcategory: inputoptional: Truepattern: */*_2.fq- output
output BAM file (automatically converted & filtered for reads that to not map)
type: mapsource: fq_forward_inputcategory: outputoptional: {}pattern: ./*.sam
Parameters¶
- extra_params
extra parameters to feed to smalt
type: stringdefault: ``optional: True- max_insertsize
Maximum allowed insertsize
type: integerdefault: 250optional: True- min_insertsize
Minimum allowed insertsize
type: integerdefault: 1optional: True- output_format
output format (sam or samsoft)
type: {}default: samoptional: True- pairtype
pair type (pe: fr/illumina short; mp: rf/illumina mate pairs or pp: ff
type: {}default: peoptional: True- threads
No threads to use
type: intdefault: 4optional: True
miscellaneous¶
- Backend
- ruff
- Author
- Mark Fiers
- Creation date
- Tue, 27 Mar 2012 10:05:40 +1300
- Modification date
- Tue, 27 Mar 2012 10:31:09 +1300