labsyspharm/miccheck

miccheck

A nextflow environment with exemplar data for testing the MCMICRO pipeline.

Prerequisites: https://docs.docker.com/get-docker/

Setting the stage

docker run -it --rm -e USER=$USER \
  -v /var/run/docker.sock:/var/run/docker.sock \
  -v /home/$USER/work:/home/$USER/work \
  labsyspharm/miccheck:1.0.0 /bin/bash

where

• -it --rm runs the container interactively and cleans up after exiting
• -e USER=$USER makes your USER environmental variable visible inside the container
• -v /var/run/docker.sock:/var/run/docker.sock enables Docker to spawn "sister" containers
• -v /home/$USER/work:/work sets up a persistent working directory for all containers

Running tests

Once inside the container, you can execute the standard tests with

nextflow run labsyspharm/mcmicro -w /home/$USER/work --in /data/exemplar-001
nextflow run labsyspharm/mcmicro -w /home/$USER/work --in /data/exemplar-002 --tma

where -w tells the pipeline to use the persistent working directory.

When adding a new feature to the pipeline, fork https://github.com/labsyspharm/mcmicro and create a new branch. The feature can then be tested on the exemplars by

nextflow run username/mcmicro -w /home/$USER/work -r newfeature --in /data/exemplar-001
nextflow run username/mcmicro -w /home/$USER/work -r newfeature --in /data/exemplar-002 --tma

replacing username with your GitHub username and newfeature with the name of the branch.