Flye output assembly_gfa in format gfa not gfa1

[AnnaSyme]

Tool issue: Flye (version 2.9.5+galaxy0).
Running on: Galaxy Australia (but seems the same in Galaxy Eu).

The current version of the tool Flye outputs a "graphical fragment assembly" in gfa format. However, downstream tools (e.g. Bandage Image) will not accept this unless the file type has been changed (e.g. to gfa1).

When I try to assign a datatype to a file, I only see the options for gfa1 or gfa2, so I'm wondering if gfa is a recognized datatype in Galaxy?

In past versions of Flye (versions 2.9.3+galaxy0 and earlier), the output of this file was set at 'txt'.

[AnnaSyme]

Edited to add: at https://help.galaxyproject.org/ I can see a few questions filed that may also relate to this issue, when I search for "gfa".

[bernt-matthias]

Indeed, there is no gfa datatype. Only gfa1 and gfa2.

https://github.com/galaxyproject/galaxy/blob/9960c312656afd345c3ee9d20a45c920264c6314/lib/galaxy/config/sample/datatypes_conf.xml.sample#L31

I hope that a new linter that will be added with the next release will reduce the number of such mistakes galaxyproject/galaxy#17600.

[bgruening]

@AnnaSyme do you know what does flye produce gfa1 or gfa2?

[AnnaSyme]

@bgruening I did auto-detect on the file and it said it was gfa1

[bernt-matthias]

bgruening/galaxytools#1556