nf-core-awsomicstest
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Scientific vocabulary similarity
Low similarity (8.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: wslh-bio
- License: mit
- Language: Nextflow
- Default Branch: main
- Size: 2.2 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 1
- Open Issues: 0
- Releases: 2
Metadata Files
README.md
![nf-core/awsomicstest]
Introduction
nf-core/awsomicstest is a bioinformatics pipeline that simply tests the functionality of a nf-core based workflow in AWS HealthOMICS.
Usage
This workflow can be installed and setup by following this procedure:
1. Setup ECR Deploy the ecr helper from here: https://github.com/aws-samples/amazon-ecr-helper-for-aws-healthomics. Once deployed using the following command and supply the containerimagemanifest.json included in this repository:
aws stepfunctions start-execution \
--state-machine-arn arn:aws:states:<aws-region>:<aws-account-id>:stateMachine:omx-container-puller \
--input file://container_image_manifest.json
2. Upload nf-core-awsomicstest workflow Upload the nf-core-awsomicstest.zip from the release into an S3 bucket accessible by AWS Health OMICS.
3. Setup the workflow in AWS using the aws management console, at the parameters step use the parameter-template.json to configure the parameters.
4. Build the Samplesheet The sample sheet needs to be csv format and have three headers and point to where the data is located in S3. Here is example:
|sample|fastq1|fastq2| |---|---|---| |TestSample01|s3://<bucket-name>/<prefix-name>/TestSample01R1.fastq.gz|s3://<bucket-name>/<prefix-name>/TestSample01R2.fastq.gz|
Now, you can run the pipeline in AWS Health Omics!
Credits
nf-core/awsomicstest was originally written by CJ Jossart.
Owner
- Name: WSLH Bioinformatics
- Login: wslh-bio
- Kind: organization
- Repositories: 4
- Profile: https://github.com/wslh-bio
Wisconsin State Laboratory of Hygiene Bioinformatics
GitHub Events
Total
- Release event: 1
- Watch event: 2
- Push event: 1
- Create event: 1
Last Year
- Release event: 1
- Watch event: 2
- Push event: 1
- Create event: 1
Dependencies
- actions/upload-artifact v3 composite
- seqeralabs/action-tower-launch v2 composite
- actions/upload-artifact v3 composite
- seqeralabs/action-tower-launch v2 composite
- mshick/add-pr-comment v1 composite
- actions/checkout v4 composite
- nf-core/setup-nextflow v1 composite
- actions/stale v7 composite
- actions/checkout v4 composite
- actions/setup-node v4 composite
- actions/checkout v4 composite
- actions/setup-node v4 composite
- actions/setup-python v4 composite
- actions/upload-artifact v3 composite
- mshick/add-pr-comment v1 composite
- nf-core/setup-nextflow v1 composite
- psf/black stable composite
- dawidd6/action-download-artifact v2 composite
- marocchino/sticky-pull-request-comment v2 composite
- actions/setup-python v4 composite
- rzr/fediverse-action master composite
- zentered/bluesky-post-action v0.0.2 composite