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Cannot use aws cli when the fargateMode is true #5835

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waynewang117 opened this issue Mar 2, 2025 · 0 comments
Open

Cannot use aws cli when the fargateMode is true #5835

waynewang117 opened this issue Mar 2, 2025 · 0 comments

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@waynewang117
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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

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