gatk4-data-processing
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools (by gatk-workflows)
| gatk4-data-processing | amazon-genomics-cli | |
|---|---|---|
| 1 | 1 | |
| 142 | 147 | |
| 4.9% | 0.7% | |
| 0.0 | 4.6 | |
| almost 2 years ago | 9 days ago | |
| wdl | Go | |
| BSD 3-clause "New" or "Revised" License | Apache License 2.0 |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
gatk4-data-processing
Posts with mentions or reviews of gatk4-data-processing.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-04-26.
-
Profiling workflows with the Amazon Genomics CLI
To run a workflow with AGC you use commands like the following - in this case I’m running the GATK data processing workflow that is included as an example when you install AGC:
amazon-genomics-cli
Posts with mentions or reviews of amazon-genomics-cli.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-04-26.
-
Profiling workflows with the Amazon Genomics CLI
This makes it difficult for steps we want to do later that involve the job-id. The JSON formatter for agc is not currently used by the agc logs workflow command. I created an issue to address this to help the team prioritize it. I could probably solve this in the short term with some regular expressions, but I’d rather not. There is another way to consistently get machine parseable output.
What are some alternatives?
When comparing gatk4-data-processing and amazon-genomics-cli you can also consider the following projects:
jq - Command-line JSON processor [Moved to: https://github.com/jqlang/jq]
sops - Simple and flexible tool for managing secrets
awscurl - curl-like access to AWS resources with AWS Signature Version 4 request signing.
Pulumi - Pulumi - Infrastructure as Code in any programming language. Build infrastructure intuitively on any cloud using familiar languages 🚀
amazon-genomics-cli-demos - Demos of what can be done with the Amazon Genomics CLI