Description

This project aims to implement MistyR as a downstream module into the MCMICRO pipeline.

Day one of the hackathon

Setup

We first evaluated which parts and outputs of MISTyR we wanted to implement and to which parameters the user should have access, to have a minimal viable project. We first agreed to implement MISTy as an option for the downstream analyis module.

• Input:
  The implementation would take two input files: the quantification file generated from the quantification module, and the markers file (used on any run of MCMICRO).

• Output:
  As a framework, MISTy allows for a large number of combinations of views, parameters and output files. In this implementation we are returning the user gains, contributions, interaction heatmap and interaction community.

Taks

• Testing the mistyR docker container.
• Figuring out how to run custom R scripts from inside the mistyR docker container.
• Preparing a wrapper R script to specify (and for the time being limit) the scope of MISTy.
• Integrating the MISTyR docker container and the wrapper R script into a standalone nextflow.
• Forking labsyspharm/mcmicro and integrating MISTY-Nextflow as a part of downstream module.
• Test it on exemplar-001
• Submitting a pull request from labsyspharm/mcmicro. :happy_face:

Day two of the hack’a ton

• Input:
  The user needs to add a column named “misty” to the markers.csv with “x” in the rows of the markers to be considered by MistyR.

Last working test

mcmicro_misty % nextflow run misty.nf -with-docker tanevesky/mistyr:latest