creates inputs.json files to be used with the LocalApp
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 |
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 bashor 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 bashBoth /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 --helpAnd 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.