Initial commit

.gitignore

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+build_docker.sh
+test_pipeline.sh
+.*.swp

100x_wes.json

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+{
+  "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": "YOUR_BUCKET_HERE",
+  "BQSR_SITES": "gs://sentieon-test/pipeline_test/reference/Mills_and_1000G_gold_standard.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/1000G_phase1.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/dbsnp_138.b37.vcf.gz",
+  "REALIGN_SITES": "gs://sentieon-test/pipeline_test/reference/1000G_phase1.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/Mills_and_1000G_gold_standard.indels.b37.vcf.gz",
+  "DBSNP": "gs://sentieon-test/pipeline_test/reference/dbsnp_138.b37.vcf.gz",
+  "PREEMPTIBLE_TRIES": "2",
+  "N_TRIES": "1",
+  "STREAM_INPUT": "True",
+  "MIN_CPU": 8,
+  "MIN_RAM_GB": 24,
+  "ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
+  "PROJECT_ID": "YOUR_PROJECT_HERE"
+}

30x_wgs.json

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+{
+  "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": "YOUR_BUCKET_HERE",
+  "BQSR_SITES": "gs://sentieon-test/pipeline_test/reference/Mills_and_1000G_gold_standard.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/1000G_phase1.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/dbsnp_138.b37.vcf.gz",
+  "REALIGN_SITES": "gs://sentieon-test/pipeline_test/reference/1000G_phase1.indels.b37.vcf.gz,gs://sentieon-test/pipeline_test/reference/Mills_and_1000G_gold_standard.indels.b37.vcf.gz",
+  "DBSNP": "gs://sentieon-test/pipeline_test/reference/dbsnp_138.b37.vcf.gz",
+  "PREEMPTIBLE_TRIES": "2",
+  "N_TRIES": "1",
+  "STREAM_INPUT": "True",
+  "ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
+  "PROJECT_ID": "YOUR_PROJECT_HERE"
+}

Dockerfile

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+FROM sentieon/sentieon:201711.01
+ARG version=201711.01
+
+RUN apt-get update && apt-get install -y \
+    bc \
+    lsb-release \
+    curl \
+    && export CLOUD_SDK_REPO="cloud-sdk-$(lsb_release -c -s)" \
+    && echo "deb http://packages.cloud.google.com/apt $CLOUD_SDK_REPO main" | tee -a /etc/apt/sources.list.d/google-cloud-sdk.list \
+    && curl https://packages.cloud.google.com/apt/doc/apt-key.gpg | apt-key add - \
+    && apt-get update && apt-get install -y google-cloud-sdk \
+    && pip install --upgrade requests
+
+ADD gc_germline.sh gen_credentials.py /opt/sentieon/
+

example.json

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+{
+  "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": "YOUR_BUCKET_HERE",
+  "ZONES": "us-central1-a,us-central1-b,us-central1-c,us-central1-f",
+  "PROJECT_ID": "YOUR_PROJECT_HERE"
+}