WORKFLOW: Basic
The Basic workflow is meant to just check if there is any indication of sequencing or sample related issues.
| Parameter Identifier | Parameter Value Type / Default | Parameter Description |
|---|---|---|
| run_subsample | String/Boolean. False | Specify whether to perform subsampling of reads (e.g. to quickly get a glimpse of the data) |
| read_subsampling | Integer. 10000 | The number of reads to subsample. |
| run_centrifuge | String/Boolean. False | Specify whether to perform Centrifuge taxonomic classification. |
| centrifuge_index | String. /path/to/default/CentrifugeIndex-DB | The path to the Centrifuge db/index. |
| centrifuge_memory | Integer. 24 | The memory (in Gb) per cpu thread to provide. |
| centrifuge_threads | Integer. 1 | The number of cpu threads to request. |
| centrifuge_timelimit | String. 00:02:00 | The time limit on the cluster job. |
| run_cleanup | String. False | Delete intermediate FASTQ files: True/False |
