Martín Beracochea

Hi, Thanks for the tool, really useful!. There seems to be a change on the output of RPS-Blast, an example line: `fig|992418.4.peg.8018 gnl|CDD|223110 26.42 159 100 6 20 165 11...

Bump to 1.0.1 - https://pypi.org/project/checkv/1.0.1/

Use GH actions / EBI gitlab to build and push the containers if there are changes.

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We want to automate the custom containers we are using to be built and pushed to quay automatically.

Performance

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# Performance bottlenecks Currently the slowest steps are: - VirSorter - Hmmscan ## Proposed solutions ### hmmscan Chunk fasta ### VirSorter There is a new version coming up in the...

Docker and CWL databases type "string"

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Running the pipeline using docker is currently blocked by the databases paths being strings instead of Directory|File. The paths change to string was required due to some issues with Toil...

MGnify has some very large studies, downloading those is problematic. With the current implementation if there is a network issue there is no way to restart the download process using...

Review the fields we are fetching from ENA and include the sample_alias

Related to issue #21

Inver the order of the taxonomic lineages on the output files

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This will close #113