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Description of feature

But still masks somehow...

Description of feature

Not called at the moment, what can be done?

Description of feature

Given a single query fasta file with sequences and a set of hmm files with corresponding reference tree and alignment, search the query sequences with all hmm files. Among hits that qualify above a bitscore and/or e-value cutoff, identify the hmm(s) for which each sequence scored best (bitscore). For every hmm, pass the assigned sequences to placement.

The pipeline will be called with a samplesheet without the queryseqfile. Query sequences will instead be passed via --queryseqfile. This combination of parameters, i.e. --input in combination with --queryseqfile, will trigger the new behaviour. Parameters, passed to hmmsearch, for minimum bitscore and maximum e-value will be added.

Description of feature

Add the possibility to specify an hmm file that both the reference and query sequences are aligned to.