Setting up a portable 16S rDNA pipeline for CBIO

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

05/23/2018

01:34 PM Feature #53: Setup a decontamination pipeline for Mark's project

Hi,
I have started constructing decontamination module on uct-cbio repository, and have named (uct-cbio/16S-rDNA-... Samson Kilaza

05/22/2018

05:13 PM Feature #52: Cleaning up current pipeline outputs for easier management downstream, finalise protocol of metadata sharing between sequencing, pipeline processing and statistical analysis

Ok Samson I've asked Shantelle also to give some input in the document. Once she has done all of us can maybe meet an... Gerrit Botha

02:12 PM Feature #54: DADA2 workflow as an additional option for processing 16S data

Hi Katie,
I think it is definitely better to keep the config and code separate as the RNASeq Nextflow pipeline. Fo... Gerrit Botha

01:54 PM Feature #54: DADA2 workflow as an additional option for processing 16S data

Gerrit I see the Nextflow implementation of DADA2 currently only consists of one .nf file, no configs etc. Shall I tr... Katie Lennard

05/21/2018

04:47 PM Feature #52: Cleaning up current pipeline outputs for easier management downstream, finalise protocol of metadata sharing between sequencing, pipeline processing and statistical analysis

Hi Samson,
I started looking at the document and added some comments on request. Can you please have a look.
Ge... Gerrit Botha