Redmine

06/07/2018

02:37 PM Setting up a portable 16S rDNA pipeline for CBIO 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 Setting up a portable 16S rDNA pipeline for CBIO 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 Setting up a portable 16S rDNA pipeline for CBIO 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

04:42 PM Setting up a portable 16S rDNA pipeline for CBIO 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

12:39 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Bug #56 (New): Get pipeline details for getting data in and out.

We need to know how we will be able to get data onto their system, and how we can retrieve the results once the run i... Jon Ambler

12:37 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Support #23 (Resolved): Test the DRAGEN GATK best practice workflow on a WGS GiaB sample

Jon Ambler

12:37 PM Testing human WGS alignment, calling and joint calling on DRAGEN hardware Support #23: Test the DRAGEN GATK best practice workflow on a WGS GiaB sample

As testing has already been completed on a gold standard sample is reported above, closing this ticket to move to ass... Jon Ambler

05/23/2018

01:34 PM Setting up a portable 16S rDNA pipeline for CBIO 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 Setting up a portable 16S rDNA pipeline for CBIO 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 Setting up a portable 16S rDNA pipeline for CBIO 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 Setting up a portable 16S rDNA pipeline for CBIO 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 Setting up a portable 16S rDNA pipeline for CBIO 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