write uncompressed corrected reads to tmp dir and only the compressed corrected reads to the output dir

[migueldiascosta]

Is your feature request related to a problem? Please describe. For generic questions use Q&A section in the Discussions forum above.

When the output corrected reads are compressed (so, without --disable-gzip-output), the uncompressed corrected reads are written to the output folder even when --tmp-dir is set.

Assuming --tmp-dir is on a faster and/or local filesystem compared to the output dir, this means the uncompressed files are first written to the slower and/or remote filesystem and then read back for compression before writing the compressed files...

Describe the solution you'd like

When --disable-gzip-output is not set and --tmp-dir is set, I would have expected the uncompressed files to be written to the tmp dir and only the compressed files written to the output dir

Describe alternatives you've considered

No response

Additional context

No response