publishDir name collision for salmon.merged.SummarizedExperiment.rds #1572
Description
Description of the bug
A path/name collision occurs for file results/star_salmon/salmon.merged.SummarizedExperiment.rds
The source of this bug is the process by name selector defined in the workflows/rnaseq/nextflow.config
rnaseq/workflows/rnaseq/nextflow.config
Lines 471 to 482 in 0bb032c
Selectors SE_GENE, SE_GENE_SCALED, SE_GENE_LENGTH_SCALED and SE_TRANSCRIPT do not apply to any process. Perhaps the underlying sub-workflow was updated but the pipeline level nextflow.config was never updated.
The bug remained unmasked possibly because the user/role under awstestfull has read, write and overwrite permissions for the publish directory. However, in my testing, I face the following error,
nextflow.processor.PublishDir - Failed to publish file: s3://***********************/553b4eed-33b7-4f16-aa5c-58f0942ad951/59/1522ee76ce0ab44216fb4057fa59b8/salmon.merged.SummarizedExperiment.rds;
to: s3://***********************/3959aa34-799f-415d-ad1d-b2a1cb79e200/553b4eed-33b7-4f16-aa5c-58f0942ad951/c1129a73-ae94-4e47-8f1b-4e65909dae45/results/star_salmon/salmon.merged.SummarizedExperiment.rds [copy]
-- attempt: 1;
reason: User: *********************** is not authorized to perform: s3:DeleteObject on resource:
"arn:aws:s3:::***********************/3959aa34-799f-415d-ad1d-b2a1cb79e200/553b4eed-33b7-4f16-aa5c-58f0942ad951/c1129a73-ae94-4e47-8f1b-4e65909dae45/results/star_salmon/salmon.merged.SummarizedExperiment.rds"
because no identity-based policy allows the s3:DeleteObject action (Service: Amazon S3;
Status Code: 403; Error Code: AccessDenied; Request ID: ***********************;
S3 Extended Request ID: ***********************/***********************/+***********************=; Proxy: null)Command used and terminal output
nextflow run nf-core/rnaseq -r 3.19.0 -profile test_full ...Relevant files
No response
System information
Cloud
nf-core/rnaseq Version 3.19.0