SRA integration for data transfer automation
- Dominant language
- Java
- Stars
- 163
- Forks
- 65
- Avg merge
- 11h 46m
- Merged PRs (30d)
- 29
Description
**GUI**
1. Add a new parameter type "SRA Run Accesion ID"
2. Such parameter shall shown as a `string` param but validated using `SRR` accession naming scheme
3. When a run is launched - it shall be set as an `input` parameter
**SRA Toolkit**
1. Add the [ncbi/sra-tools](https://github.com/ncbi/sra-tools) binaries to the distribution bucket at `cloud-pipeline-oss`
2. Add installation/configuration steps to the `launch.sh` dependencies installation
**Data localization**
1. Tune the localization logic to parse `SRR` accession naming scheme
2. If `SRR` ID is matched - fetch and unpack data using [ncbi/sra-tools](https://github.com/ncbi/sra-tools)
3. Resulting FASTQ/Contents directories locations shall be exported to the environment variables. Original parameter name/value shall be persisted
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