fastx_clipper¶
run fastx_clipper
Commands¶
- clean
- Remove all job data, not the Moa job itself
- run
- run fastx_clipper
Filesets¶
- input
- fastq input files directory
output
type: mapsource: inputcategory: outputoptional: {}pattern: ./*.fq
Parameters¶
- adaptor
ADAPTER string. default is CCTTAAGG (dummy adapter).
type: stringdefault: CCTTAAGGoptional: True- adaptor_and_bases
Keep the adapter and N bases after it.
type: integerdefault: 0optional: True- compress_output
Compress output with GZIP.
type: booleandefault: Falseoptional: True- debug_output
DEBUG output.
type: booleandefault: Falseoptional: True- help
help screen
type: booleandefault: Falseoptional: True- keep_unknown_nuc_seq
keep sequences with unknown (N) nucleotides. default is to discard such sequences.
type: booleandefault: Falseoptional: True- out_adaptor_only_seq
Report Adapter-Only sequences.
type: booleandefault: Falseoptional: True- rm_clipped_seq
Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).
type: booleandefault: Falseoptional: True- rm_non_clipped_seq
Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).
type: booleandefault: Falseoptional: True- rm_short_seq
discard sequences shorter than N nucleotides. default is 5.
type: integerdefault: 5optional: True- verbose
Verbose - report number of sequences. If [-o] is specified, report will be printed to STDOUT. If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.
type: booleandefault: Falseoptional: True
miscellaneous¶
- Backend
- ruff
- Author
- Mark Fiers, Yogini Idnani
- Creation date
- Wed Dec 06 17:06:48 2010
- Modification date
- unknown