Less common options for the pipeline, typically set in a config file.
| Parameter |
Description |
Type |
Default |
Required |
Hidden |
publish_dir_mode |
Method used to save pipeline results to output directory. HelpThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details. |
string |
copy |
|
True |
| Parameter |
Description |
Type |
Default |
Required |
Hidden |
samplesheet |
|
string |
None |
True |
|
enable_conda |
use conda (not supported) |
boolean |
|
|
|
min_contig_length |
Minimum contig length to keep |
string |
5000 |
|
|
reference_proteins |
Reference proteins for miniprot |
string |
'/dss/dsslegfs01/pn73so/pn73so-dss-0000/becker_common/reference_genomes/Arabidopsis/Col-CEN/Col-CEN_v1.2_proteins.fasta' |
|
|
out |
Directory for outputs |
string |
./results |
|
|
porechop |
Run porechop |
boolean |
|
|
|
exclude_pattern |
Pattern to exclude for HRP |
string |
ATMG |
|
|
nevm |
not used |
string |
10 |
|
True |