https://github.com/wtsi-hgi/nf_tower_irods_to_lustre
https://github.com/wtsi-hgi/nf_tower_irods_to_lustre
Last synced: about 2 months ago
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- Host: GitHub
- URL: https://github.com/wtsi-hgi/nf_tower_irods_to_lustre
- Owner: wtsi-hgi
- License: gpl-3.0
- Created: 2022-05-24T15:09:05.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2025-01-10T13:29:27.000Z (4 months ago)
- Last Synced: 2025-01-26T18:48:12.218Z (3 months ago)
- Language: Nextflow
- Size: 118 KB
- Stars: 1
- Watchers: 3
- Forks: 1
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# iRODS to lustre pipeline
This pipeline is designed to be run using Nextflow Tower but it should work as a standalone.
The pipeline can accept various different inputs
1. Study_id - get all CRAMS from a specific iRODS study based on its ID
2. Study_id and Run id - get all CRAMS from a specific run in a study based on their IDs
3. csv_samples - will iget samples listed one-per-line in input file "samples.tsv"
4. google_spreadsheet - will iget samples listed one-per-line in google spreadsheet
## How to use
Tutorial is available [here](https://hgi-projects.pages.internal.sanger.ac.uk/documentation/docs/tutorials/irods-to-lustre/)
## Development
### Setup
Create and activate an environment
```bash
python -m venv ./venv
source ./venv/bin/activate
```
Install both library dependencies and the dependencies needed for testing:
```bash
pip install -r requirements/imeta_study.txt
pip install -r tests/pytest/requirements.txt
```
Install nextflow and nf-test
```bash
curl -s https://get.nextflow.io | bash
mv nextflow ./venv/bin/
```
```bash
curl -fsSL https://code.askimed.com/install/nf-test | bash
mv nf-test ./venv/bin/
```
You also need iRODS access to `/seq` and `/seq-dev` zones.
### Testing
Currently, tests rely on iRODS state, proper encapsulation needed.
Test python scripts
```bash
export PYTHONPATH=$PYTHONPATH:$(pwd)
export IRODS_ENVIRONMENT_FILE=$(ls ~/.irods/irods_environment.seq-dev.json)
# iinit if you use PAM auth
pytest tests/pytest/
```
Test nextflow scripts
```bash
export IRODS_ENVIRONMENT_FILE=$(ls ~/.irods/irods_environment.json)
# iinit if you use PAM auth
nf-test test tests/nf-test/
```