pregap¶

Pregap

Run Pregap. Note that running phrap could be a part of this.

Commands¶

clean: Remove all job data, not the Moa job itself, note that this must be implemented by the template.
run: no help defined

cloning_vector: File containing the cloning vector

type: file

default: ``

optional: False
ecoli_screenseq: File containing ecoli screen sequences

type: file

default: ``

optional: False
input_dir: Directory with the input data

type: string

default: ``

optional: False
input_pattern: file name pattern

type: string

default: ``

optional: False
quality_value_clip: quality cutoff

type: integer

default: 10

optional: True
repeat_masker_lib: File with a repeatmasker library

type: file

default: ``

optional: False
sequencing_vector: File containing the sequencing vector

type: file

default: ``

optional: False
template: the template pregap config file to use. if not defined, Moa tries ./files/pregap.config.

type: file

default: ./files/pregap.config.

optional: True
vector_primerfile: File with the vector primers

type: file

default: ``

optional: False