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add one test case for running workflow in rdpc
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lindaxiang committed Apr 23, 2024
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Expand Up @@ -23,6 +23,12 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool
```

5. Start running your own analysis!

If you are getting the input data from & sending output data to ICGC-ARGO data center, and you have valid api_token, you can run the workflow with:
```bash
nextflow run icgc-argo-workflows/prealnqc -profile <rdpc,rdpc_qa,rdpc_dev>,standard --api_token <YOUR_API_TOKEN> --study_id <STUDY_ID> --analysis_ids <ANALYSIS_IDS>
```
Otherwise, you can provide the path to the input data in `samplesheet.csv` and run the workflow with:
```bash
nextflow run icgc-argo-workflows/prealnqc -profile standard --input samplesheet.csv --outdir <OUTDIR>
```
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