A subworkflow for

unzipping fasta, cleaning and then index/sizes generation

(and I'd suggest dict generation too) : github.com/nf-core/modules/pull/12663 definitely not

GUNZIP_FASTA_INDEX

, because

FASTA

should be first.

so....

fasta_gunzip_index

then?

well, I think it might gain more tools

I liked your suggestion of

FASTA_PREPARE

well enough, though I'd prefer a slightly more apt description maybe

FASTA_INDEX_PREPARE

?

Apologies, I've been on holiday the past week and come back to this today. I've added

SAMTOOLS_DICT

, swapped out

GAWK

for

SEQKIT_SEQ

and added

SEQKIT_REPLACE

for sequence and header cleaning.

FASTA_PREPARE

could make sense, like you say more could be added and it is a nice concise descriptor

FASTA_CLEAN_FAI_INDEX

is the only way I can see it being more verbose and helpful.

What other indexers would you reasonably want to run? I think

samtools faidx

would be the standard option - could always extend if needed. What about

FASTA_CLEAN_FAIDX

?

More of an open invitation,

FASTA_CLEAN_FAIDX

makes sense yeah