nextflow-io / nextflow-io/nextflow
Cannot use aws cli when the fargateMode is true
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- Dominant language
- Groovy
- Stars
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Description
Bug report
Cannot use aws cli when the fargateMode is true。
Expected behavior and actual behavior
We plan to run nextflow on AWS batch and configured the cliPath. But it doesn't work. Nextflow still use s5cmd to download files from S3 bucket.
nextflow.config
'''
aws.batch.platformType = 'fargate'
aws.batch.cliPath = '/usr/bin/aws'
'''
" s5cmdPath = fargateMode ? parses5cmdPath(opts.cliPath as String) : null"
https://github.com/nextflow-io/nextflow/blob/master/plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy#L105
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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- Open a pull request that references the issue number.
Research direction
Read plugins/nf-amazon/src/main/nextflow/cloud/aws/config/AwsBatchConfig.groovy around line 105 first, using the reported fargate platformType and cliPath configuration to trace the selected download tool. Done means AWS Batch in Fargate mode uses the configured AWS CLI rather than s5cmd for S3 downloads.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- aws, groovy
- Domain
- cloud
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 50/100