local_app_prepper

creates inputs.json files to be used with the LocalApp

Introduction 💬

Running the LocalApp requires the specification of a least one inputs.json file containing the configuration as well as input and output options. To make running the LocalApp more efficient, the local_app_prepper will generate several inputs.json files:

inputs.json	description
demultiplex.json	running the initial steps to demultiplex the sequencing data
tso500_<sample id>.json	running the DNA/RNA workflow of the TSO500 pipeline from .fastq files
gather.json	running the Gather workflow to combine all results into a single directory

Dependencies 💼

Usage 🚀

The docker image inpred/local_app_prepper:latest is available at dockerhub. The recommended way of running the tool is as a container (docker, singularity/apptainer).

Start your docker container like so:

$ docker run --rm -it -v /path/to/runfolder:/containerpath/to/runfolder:ro inpred/local_app_prepper:latest bash

or if you are more a apptainer/singularity kind of person:

$ apptainer run -B /path/to/runfolder:/containerpath/to/runfolder:ro docker://inpred/local_app_prepper:latest bash
# OR
$ singularity run -B /path/to/runfolder:/containerpath/to/runfolder:ro docker://inpred/local_app_prepper:latest bash

Both /path/to/runfolder and /containerpath/to/runfolder should be replaced with the actual path to the run folder and the path you chose for mounting the folder inside the container, respectively.

Once you are inside the container, you can execute the following to get some help text:

$ local_app_prepper.py --help

And to produce .json files, simply run:

$ local_app_prepper.py -i /containerpath/to/runfolder -s <sample 1 id>,<sample 2 id>,...

/containerpath/to/runfolder should be replaced with the actual path you mounted the run folder at inside the container and <sample 1 id> etc. should be a comma-separated list of your sample ids.