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uclanelsonlab / nl-rna-seq_wf

RNA-seq for rare diseases pipeline using nextflow
MIT License
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Output not uploaded to the S3 bucket #7

Closed ricorona closed 2 days ago

ricorona commented 2 days ago

After an apparent successful run, the output was not found in the selected S3 bucket.

  1. Is it a prerequisite that the S3 bucket, including the "proband" folder need to exist? If so, it should be changed to creating the folder during the run.
  2. If the purpose of the "proband" input is to select the folder on which the output will be saved, then it has to be changed to "family_id", because the main folder is not the "proband ID" (e.g. SH1311-P), but the "family ID" (e.g. SH1311).
geocarvalho commented 2 days ago

@ricorona It should create the folder directory using the proband parameter (e.g. SH1311) that I use as the "family ID". Can you send the command you used so I can troubleshoot it?

geocarvalho commented 2 days ago

The problem was the s3 path ending with /, not expected by the script when it creates the directory (e.g.:/path/to//proband/data). Maybe we can do some path check in the future.