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kfuku52 / amalgkit

RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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getfastq download options #111

Closed kfuku52 closed 1 year ago

kfuku52 commented 1 year ago

@Hego-CCTB Could you remind me why those options are set to no by default? I thought they should be yes by default and users should deactivate it if they have a particular reason to avoid some of them.

  --ncbi yes|no         default=no: Download SRA files using wget from NCBI cloud, if available.
  --aws yes|no          default=no: Download SRA files from Amazon Cloud (AWS), if available.
  --gcp yes|no          default=no: Download SRA files from Google Cloud (GCP), if available.
Hego-CCTB commented 1 year ago

No particular good reason. When I implemented those options I treated them as an alternative to the back then only option. I preserved the original behaviour by making these optional. But yeah, I exclusively use these options myself anyways, so might as well turn them on by default. Will come with the next update.

Hego-CCTB commented 1 year ago

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