I have been using the galaxy API to upload files into a library (using a
local folder for library import) and running a workflow into a history. I
have been following the example scripts that come with galaxy.

When I upload a gzipped fastq file, in autodetection mode (linking the
file and not copying, to be faster), the file is not detected as fastq.
Even if I explicitly say that it is a fastq, the file is uploaded as a
fastq but with its contents gzipped (so downstream analysis fail).

Nonetheless, if I do this manually through the interface, the file is
unzipped correctly.

Any idea how can I upload the gzipped fastq through the API so that it can
be used properly?

Thank you.

Daniel Sobral
Next Generation Sequencing Data Analyst
IGC - Instituto Gulbenkian de Ciencias
e-mail dsob...@igc.gulbenkian.pt

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