BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago

Adds script `scripts/labkey_to_snakemake.py` which
- maps LabKey table fields to Snakemake parameters
- assembles required parameters from the table data
- infers required parameters from the input data
- produces files `config.yaml` and `samples.tsv` required by the Snakemake pipeline

A self-contained integration test for the script is located at `tests/test_scripts_labkey_to_snakemake` (execute script `test.sh`) and was added to the CI/CD pipeline.

Note that intermittent changes to the `master` branch were merged into this branch to forego conflicts during merging.

Closes #39

BIOPZ-Gypas Foivos authored 5 years ago and Alex Kanitz committed 5 years ago

- replace corrupt input files
- add script that runs locally named `run_test.sh` in the snakemake directory
- add script to CI/CD pipeline
- fix typo in `paired_end.snakefile`
- update samples.tsv with fake adapter `XXXXXXX` when we do not want to trim them