No `fastq_dir` specified or no samples found in folder. Output into S3//

[LucFrancisENX]

Description of the bug

Hello, thanks for the great pipeline.

I am trying to run the test profile with the workDir set to an S3 bucket. The untar of the spaceranger output works fine, and the fastq.gz files are visible within the output directory.

However, within the nextflow.log file I then get this error:

b-17 11:47:38.537 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 2; name: NFCORE_SPATIALVI:SPATIALVI:INPUT_CHECK:UNTAR_SPACERANGER_INPUT (fastq_dir.tar.gz); status: COMPLETED; exit: 0; error: -; workDir: s3://{workDir}/9f/26ae4916198fdd34c27e346525e200] Feb-17 11:47:38.587 [Actor Thread 5] DEBUG nextflow.Nextflow - No such file or directory: /{workDir}/fastq_dir -- Skipping visit Feb-17 11:47:38.624 [Actor Thread 5] ERROR nextflow.extension.OperatorImpl - @unknown nextflow.exception.WorkflowScriptErrorException: No fastq_dir specified or no samples found in folder.

Is it possible that the s3:// prefix is dropped at some point, and this is why fastq_dir cannot be found?

Thanks for your help

Command used and terminal output

Relevant files

No response

System information

No response

[cavenel]

Hi @LucFrancisENX sorry for the slow answer here, unfortunately I don't have an s3 bucket to test, so I can not try to put the work dir on s3. Once I get access to one, I will try to reproduce (as well as https://github.com/nf-core/spatialvi/issues/94) and let you know. If you find a solution before that feel free to share here!