A repository containing code relating to per sample quality control of samples submitted to mscape. A climb ID is taken as input, and basic QC metrics are calculated for the given sample. QC metrics are then added to an analysis table in Onyx in json format.
Clone repo:
git clone git@github.com:ukhsa-collaboration/mscape-sample-qc.git
cd mscape-sample-qc
conda create -n mscape_sample_qc python
conda activate mscape_sample_qc
User installation:
pip install .
For developers:
pip install -e ".[dev]"
| Flag | Required? | Description |
|---|---|---|
| --help, -h | No | Display help message |
| --input , -i | Yes | Climb ID for sample |
| --config, -c | No | Specify QC metrics config file to use. If not specified, the default will be used |
| --output, -o | Yes | Folder to save QC results to |
| --server, -s | Yes | Specify server code is being run on. Options: mscape, synthscape |
| --no-onyx | No | Use this option to write QC results to file with no onyx steps |
| --store-onyx | No | Use this option to write QC results to file and create an onyx analysis object that is written to file for later upload |
| --test-onyx | No | Use this option to write QC results to file and test submitting an onyx analysis object to onyx |
| --prod-onyx | No | Use this option to write QC results to file and submit an onyx analysis object to onyx |
| --version, -v | No | Use this option to see the version of QC metrics. |
Example command using default config file and output QC results file to current directory:
qc_sample --input <sample_id> --output . --server "synthscape" --no-onyx
Example command specifying config file and output dir, and testing submission to onyx:
qc_sample --input --config </path/to/config/config_file.yaml> --output </path/to/results/> --server synthscape --test-onyx