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Hi,
dsub only includes --image to include a docker image, but I need to add more parameters with docker image to run fuse and fusera (as below)? How can I add these parameters?
sudo docker run --r…
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Hello,
I am curious to see what the default cromwell conf file is (the one referenced in wdl_runner.py as CROMWELL_CONF if the user doesn't overwrite the env variable). The reason is that I want to …
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I'm using this script:
```
#!/bin/bash
# Parameters to replace:
# The GOOGLE_CLOUD_PROJECT is the project that contains your BigQuery dataset.
GOOGLE_CLOUD_PROJECT=psjh-eacri-data
INPUT_PATTER…
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**Snakemake version**
`7.18.2`
**Describe the bug**
When a job fails on GLS the stdout/stderr from the instance is captured and uploaded to the specified bucket. However, if the stderr/stdo…
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The input xxxx.g.vcf.gz file was generated using the BAM to VCF Cromwell pipeline: [https://github.com/broadinstitute/wdl-runner](url)
When I ran vcf_to_bq without --run_annotation_pipeline - it r…
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I'm trying to run multiple pipelines that all read the same data (~20TB) . Copying this to all containers seems unreasonable and the best way I could think off is to put this on a shared read-only PD.…
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Certain pipelines need to access containers in private gitlab registries. Pushing images as an intermediate step to google built in registries is not a desired step due to security & maintenance polic…
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I'm using Cromwell v87 on GCP Genomics API. When submitting a job, the error I got is the following:
```
Caused by: java.lang.IllegalStateException: You are currently running with version 2.2.…
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https://docs.bigpicture.io/docs/free-datasets/companies
They distributed this dataset as a "free dataset", although the download requires registration, and the dataset is described as scraped data.…
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I learn about Snakemake and Google Cloud (GCP) Life Sciences API and there are 4 different features are very useful to GCP users. Here are my suggestions:
1. Shared VPC support - in most large acc…