Setting up a portable 16S rDNA pipeline for CBIO

06/22/2018

02:51 PM Feature #54: DADA2 workflow as an additional option for processing 16S data

The following updates have been made:
1. *Run in parallel where possible (i.e. one job/sample*) - done
2. *Run on... Katie Lennard

06/07/2018

02:37 PM Feature #53: Setup a decontamination pipeline for Mark's project

Hi,
I have prepared scripts for the detection of contaminants [detect.sh] and removal of contaminant [decont.sh] ... Samson Kilaza

11:03 AM Feature #54: DADA2 workflow as an additional option for processing 16S data

Good progress Katie, I will make a try at some point.
Samson
Katie Lennard wrote:
> The pipeline is now up a... Samson Kilaza

10:46 AM Feature #54: DADA2 workflow as an additional option for processing 16S data

The pipeline is now up and running. Several features were added to make the pipeline more user-friendly:
1. Include ... Katie Lennard

06/04/2018

05:37 PM nextflow.log.txt

nextflow.log for testrun matching screenshot Katie Lennard

05:30 PM Screen Shot 2018-06-04 at 5.30.21 PM.png

Test pipeline execution summary on hex Katie Lennard

04:42 PM Feature #54: DADA2 workflow as an additional option for processing 16S data

The DADA2 Nextflow pipeline has now been customized for use on UCT hex.
Major updates from originally shared pipeli... Katie Lennard