hello, I’m still in the phase of how to connect the subworkflow that @German Vallejo proposed about filling the mapping consensus sequence with the abacas consensus, using evolutionary priors as guidance. the subworkflow needs three mandatory input files: • genome reference fasta • consensus fasta • abacas (assembly) fasta The subworkflow can not run if any of the following flags are passed:

skip_consensus

,

skip_assembly

and

skip_abacas

. So the variables/channels to get are: •

PREPARE_GENOME.out.fasta

for the reference genome. • The consensus is chosen based on the flag

consensus_caller

. SO the channel is either

CONSENSUS_BCFTOOLS.out.consensus

(not used so far only emitted) or

CONSENSUS_IVAR.out.consensus

(same as above). • Assemblers are chose based on the flag

assemblers

. all three option can run at the same time or any cobination. Sorry for the long introduction, but the question I have is on the third input (ABACAS) @German Vallejo suggested that whatever assembler is asked from the user the subworflow is run on it. So basically run it multiple times (with alias and if controlling each call) or only once but with an internal channel organization that takes into account the presence of multiple assembly fasta file for each entry (sample if I’m not mistaken). Has anyone a preference or suggestion or solution etc. ? i wanted some feedback before starting implementing.

I think that if you

only once but with an internal channel organization that takes into account the presence of multiple assembly fasta file

the possiblity of changing the prams for PriorCons for each assembler might be difficult. I don't know if people might run it with some params for unicycler and other params for spades, as I'm not familiar with runnin PriorCons.

i see good point, then we will discuss and see what fits best for priorcons. thank you.

Thank you all!