Skip to content

Find CI test dataset for binner "COMEBin" & "MetaBinner" #884

@d4straub

Description

@d4straub

Description of feature

COMEBin

Binner COMEBin was added in #875 but is currently not activated in any test profile. This is because it appears to require larger datasets to function. With -profile test_full it does function though.

As a note, ext.args = "-b 20" (default 1000) helps with test data, as in ziyewang/COMEBin#4. However, the binner fails later after: "[CheckM - analyze] Identifying marker genes in bins.", so it doesnt make it work all the way through.

Additionally, GPU optimization might be beneficial for runtimes (which seem at this point quite high!).

MetaBinner

Binner MetaBinner was added in #881 but is currently not activated in any test profile.
This is because it appears to require larger datasets to function. It also fails with -profile test_full. nf-core/bacass's dataset for test_full works with co-assembly as described in #881 (but COMEBin fails!).

Metadata

Metadata

Assignees

No one assigned

    Labels

    enhancementNew feature or request

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions