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Workshop on Workflow Platforms
2-3 April 2020
Table of Contents
Logistics
Agenda
https://docs.google.com/document/d/1Od0JzTduih7DIlaIoYS-MnfFUl1UVmy6DprqhBlqAV8
Zoom details
Please make sure that you have your name in Zoom
Feedback survey
https://www.surveymonkey.co.uk/r/KLWJ285
Markdown cheatsheet
https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet
Session I: Problems/Solutions of RI
? encryption and authorization level
? reproducibility
EncFS - an Encrypted Filesystem
Session II: Workflow Management Systems (WMS)
nf-core licences nf-core/<pipelinename>
for example (relies on anaconda API)As Björn mentioned, Snakemake has a lower barrier for entry for users that are already experienced in Python.
You don't actually need to know any Java/Groovy to use Nextflow.
Nextflow seems to have better cloud support.
You also have to remember that both Snakemake and Nextflow will allow you to run bash, R, Perl scripts embedded within the workflow too.
Session III: Breakouts
Room 1 - Galaxy
Participants
Where to find tools?
How to integrate a Shiny app (https://shiny.rstudio.com)
Validation of Yaml format
Back end
Computational resources distribution
CWL in Galaxy?
Reproducibility and Traceability
record in the DB for every tool run
Python library to interact with Galaxy
https://bioblend.readthedocs.io/en/latest/
BioBlend – a Python (3.5, 3.6, 3.7 and 3.8) library for interacting with Galaxy and CloudMan APIs
Data transfer docs
ftp-upload
Tool update
Meta job scheduler
BioBlend API: link
Jupyter Notebook interaction with Galaxy
Room 2 - Nextflow
Participants
nf-core/configs
:Session IV: Summary & Discussion