Add optional steps to genome_submit subworkflow to handle metadata (checkm2) #7
Description
Description of feature
Completeness and contamination calculation
Subworkflow described https://docs.google.com/document/d/1yqJkbkSeLT0ci9j8HAhC41FjRK-c0f7iN_cOv-dgLcE/edit?tab=t.0 Page 5.
Now current subworkflow https://github.com/nf-core/seqsubmit/blob/dev/workflows/genomesubmit.nf takes all metadata as input samplesheet. We need to allow some metadata be missing and pipeline should detect it and generate.
For example, if user didn't provide taxonomy - seqsubmit/genomesubmit should run CAT/BAT to assign taxonomy for mags/bins.
Difficulty: Hard/Very Hard/Very long