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Failed to cleanup work dir by aws-batch nf-amazon plugin #3145

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bounlu opened this issue Aug 24, 2022 · 2 comments
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Failed to cleanup work dir by aws-batch nf-amazon plugin #3145

bounlu opened this issue Aug 24, 2022 · 2 comments

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@bounlu
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bounlu commented Aug 24, 2022

I want to cleanup work dir after successful run but it fails on AWS even though I specify cleanup flag and nf-amazon plugin in my config:

cleanup = true

plugins {
	id '[email protected]'
}

...

nextflow run nf-core/rnaseq \
-latest \
-profile docker \
--genome GRCh38 \
--input 'samplesheet_rnaseq.csv' \
--outdir 's3://nextflow/rnaseq/results/' \
-bucket-dir 's3://nextflow/rnaseq/work/' \
-work-dir 's3://nextflow/rnaseq/work/' \
-c 'custom.config' \
-r master \
-resume

...

WARN: Unable to start plugin 'nf-amazon' required by s3://nextflow/rnaseq/work/28/1b59694ba5e2f4ef93715e33c3cdc2
WARN: Failed to cleanup work dir: s3:///nextflow/rnaseq/work

@bounlu bounlu changed the title Failed to cleanup work dir Failed to cleanup work dir by aws-batch nf-amazon plugin Sep 13, 2022
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stale bot commented Mar 18, 2023

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

@stale stale bot added the stale label Mar 18, 2023
@pditommaso
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Closing in favour of #3645

@bentsherman bentsherman linked a pull request Apr 5, 2023 that will close this issue
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3 participants