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Update examples and documentation.
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Also update container version
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@DonFreed
DonFreed committed Mar 26, 2021
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38 changes: 22 additions & 16 deletions README.md
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Expand Up @@ -106,38 +106,42 @@ The runner script accepts a JSON file as input. In the repository you downloaded
"FQ1": "gs://sentieon-test/pipeline_test/inputs/test1_1.fastq.gz",
"FQ2": "gs://sentieon-test/pipeline_test/inputs/test1_2.fastq.gz",
"REF": "gs://sentieon-test/pipeline_test/reference/hs37d5.fa",
"OUTPUT_BUCKET": "gs://BUCKET",
"OUTPUT_BUCKET": "YOUR_BUCKET_HERE",
"ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
"PROJECT_ID": "PROJECT_ID",
"EMAIL": "EMAIL"
"PROJECT_ID": "YOUR_PROJECT_HERE",
"REQUESTER_PROJECT": "YOUR_PROJECT_HERE",
"EMAIL": "YOUR_EMAIL_HERE"
}
```

The following table describes the JSON keys in the file:

| JSON key | Description |
| ------------- | ----------------------------------------------------------------------------- |
| FQ1 | The first pair of reads in the input fastq file. |
| FQ2 | The second pair of reads in the input fastq file. |
| BAM | The input BAM file, if applicable. |
| REF | The reference genome. If set, the reference index files are assumed to exist. |
| OUTPUT_BUCKET | The bucket and directory used to store the data output from the pipeline. |
| ZONES | A comma-separated list of GCP zones to use for the worker node. |
| PROJECT_ID | Your GCP project ID. |
| EMAIL | Your email |
| JSON key | Description |
| ----------------- | ----------------------------------------------------------------------------- |
| FQ1 | The first pair of reads in the input fastq file. |
| FQ2 | The second pair of reads in the input fastq file. |
| BAM | The input BAM file, if applicable. |
| REF | The reference genome. If set, the reference index files are assumed to exist. |
| OUTPUT_BUCKET | The bucket and directory used to store the data output from the pipeline. |
| ZONES | A comma-separated list of GCP zones to use for the worker node. |
| PROJECT_ID | Your GCP project ID. |
| REQUESTER_PROJECT | A project to bill when transferring data from Requester Pays buckets. |
| EMAIL | Your email |

The `FQ1`, `FQ2`, `REF`, and `ZONES` fields will work with the defaults. However, the `OUTPUT_BUCKET`, `PROJECT_ID`, and `EMAIL` fields will need to be updated to point to your specific output bucket/path, Project ID, and email address.
The `FQ1`, `FQ2`, `REF`, and `ZONES` fields will work with the defaults. However, the `OUTPUT_BUCKET`, `PROJECT_ID`, `REQUESTER_PROJECT`, and `EMAIL` fields will need to be updated to point to your specific output bucket/path, Project ID, and email address.

<a name="run"/>

### Run the example pipelines

Edit the `OUTPUT_BUCKET`, `PROJECT_ID`, and `EMAIL` fields in the `examples/example.json` to your output bucket/path, the GCP Project ID that you setup earlier, and email you want associated with your Sentieon license. By supplying the `EMAIL` field, your PROJECT_ID will automatically receive a 14 day free trial for the Sentieon software on the Google Cloud.
Edit the `OUTPUT_BUCKET`, `PROJECT_ID`, `REQUESTER_PROJECT`, and `EMAIL` fields in the `examples/example.json` to your output bucket/path, the GCP Project ID that you setup earlier, and email you want associated with your Sentieon license. By supplying the `EMAIL` field, your PROJECT_ID will automatically receive a 14 day free trial for the Sentieon software on the Google Cloud.

You after modifying the `examples/example.json` file, you can use the following command to run the DNAseq pipeline on a small test dataset.
```bash
python runner/sentieon_runner.py examples/example.json
python runner/sentieon_runner.py --requester_project $PROJECT_ID examples/example.json
```
The `--requester_project` argument will configure the software to use the specified PROJECT_ID when polling input files locally. Alternatively, you might set `--no_check_inputs_exist` to skip input file polling.


<a name="understand"/>

Expand Down Expand Up @@ -278,6 +282,7 @@ The `CALLING_ALGO` key key can be change to `TNsnv`, `TNhaplotyper`, `TNhaplotyp
| EMAIL | An email address to use to obtain an evaluation license for your GCP Project |
| SENTIEON_KEY | Your Sentieon license key (only applicable for paying customers) |
| PROJECT_ID | Your GCP Project ID to use when running jobs |
| REQUESTER_PROJECT | A project to bill when transferring data from Requester Pays buckets |
| PREEMPTIBLE_TRIES | Number of attempts to run the pipeline using preemptible instances |
| NONPREEMPTIBLE_TRY | After `PREEMPTIBLE_TRIES` are exhausted, whether to try one additional run with standard instances |

Expand Down Expand Up @@ -343,6 +348,7 @@ The `CALLING_ALGO` key key can be change to `TNsnv`, `TNhaplotyper`, `TNhaplotyp
| EMAIL | An email address to use to obtain an evaluation license for your GCP Project |
| SENTIEON_KEY | Your Sentieon license key (only applicable for paying customers) |
| PROJECT_ID | Your GCP Project ID to use when running jobs |
| REQUESTER_PROJECT | A project to bill when transferring data from Requester Pays buckets |
| PREEMPTIBLE_TRIES | Number of attempts to run the pipeline using preemptible instances |
| NONPREEMPTIBLE_TRY | After `PREEMPTIBLE_TRIES` are exhausted, whether to try one additional run with standard instances |

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1 change: 1 addition & 0 deletions examples/100x_wes.json
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Expand Up @@ -9,5 +9,6 @@
"STREAM_INPUT": "True",
"ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
"PROJECT_ID": "YOUR_PROJECT_HERE",
"REQUESTER_PROJECT": "YOUR_PROJECT_HERE",
"EMAIL": "YOUR_EMAIL_HERE"
}
1 change: 1 addition & 0 deletions examples/30x_wgs.json
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Expand Up @@ -9,5 +9,6 @@
"STREAM_INPUT": "True",
"ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
"PROJECT_ID": "YOUR_PROJECT_HERE",
"REQUESTER_PROJECT": "YOUR_PROJECT_HERE",
"EMAIL": "YOUR_EMAIL_HERE"
}
1 change: 1 addition & 0 deletions examples/30x_wgs_ccdg.json
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Expand Up @@ -9,5 +9,6 @@
"STREAM_INPUT": "True",
"ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
"PROJECT_ID": "YOUR_PROJECT_HERE",
"REQUESTER_PROJECT": "YOUR_PROJECT_HERE",
"EMAIL": "YOUR_EMAIL_HERE"
}
1 change: 1 addition & 0 deletions examples/example.json
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Expand Up @@ -5,5 +5,6 @@
"OUTPUT_BUCKET": "YOUR_BUCKET_HERE",
"ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
"PROJECT_ID": "YOUR_PROJECT_HERE",
"REQUESTER_PROJECT": "YOUR_PROJECT_HERE",
"EMAIL": "YOUR_EMAIL_HERE"
}
1 change: 1 addition & 0 deletions examples/tn_example.json
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Expand Up @@ -7,6 +7,7 @@
"OUTPUT_BUCKET": "YOUR_BUCKET_HERE",
"ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
"PROJECT_ID": "YOUR_PROJECT_HERE",
"REQUESTER_PROJECT": "YOUR_PROJECT_HERE",
"PIPELINE": "SOMATIC",
"CALLING_ALGO": "TNhaplotyper",
"EMAIL": "YOUR_EMAIL_HERE"
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2 changes: 1 addition & 1 deletion runner/runner_default.json
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Expand Up @@ -34,7 +34,7 @@
"CPU_PLATFORM": "Intel Broadwell",
"PROJECT_ID": null,
"REQUESTER_PROJECT": null,
"DOCKER_IMAGE": "sentieon/sentieon-google-cloud:0.2.3",
"DOCKER_IMAGE": "sentieon/sentieon-google-cloud:0.2.4",
"CALLING_ARGS": null,
"CALLING_ALGO": "Haplotyper",
"DNASCOPE_MODEL": "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModelBeta0.4a-201808.05.model",
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