[BUG]: using manifest file requires gzipped input

[ptrebert]

Describe the bug If the input is provided as manifest file, then the execution fails

gzip: /PATH-TO-FASTA/assembly.unassigned.fasta.gz: No such file or directory
Error: Process failed with retcode 123: ['xargs', '-n1', 'gzip', '-cdf'])

because the file extension .gz is silently appended to the file name. Gzipping the individual files listed in the manifest then works.

To Reproduce Prepare manifest file with uncompressed input (file extension .fasta in the above case)

Software versions (please complete the following information): See #31

Log Files not needed

Additional context Remark: in case a manifest file is only recognized on the basis of the file extension .mft (this is given in the usage examples in the wiki), it should be explicitly documented in the wiki. I haven't tested the behavior explicitly.

Best, Peter

[pstrope]

Hi Peter, Regarding the manifest file:

• the option was only introduced to support our submission screening process, and given the added complexity necessary for supporting the path mapping needed with containers we're removing support for the option at this time.

Thank you for your feedback!

Pooja

[ptrebert]

I see, too bad that option will be removed. Thanks for letting me know.