fasta_hmmsearch_rank_fastas

Run hmmsearch and output separate fasta files for top scoring hits to each profile

hmmersearchrankfasta

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fasta_hmmsearch_rank_fastas

Description

Run hmmsearch and output separate fasta files for top scoring hits to each profile

Input

name

description

pattern

`ch_hmms`

The input channel containing hmm profiles
Structure: [ val(meta), path(hmm) ]

*.{hmm}

`ch_fasta`

The input channel containing sequences to be searched and ranked

`save_domtblout`

Whether hmmsearch should also write and emit its per-domain hit table (–domtblout)

Output

name

description

pattern

`hmmrank`

Channel containing the TSV file from ranking hmmsearch hits.
When save_domtblout is set, the table also carries the target and profile lengths
and, for each of the three coordinate sets, the bounds of the match, the size of the
union of the pair’s domains, and the number of disjoint pieces it falls into.
Structure: [ val(meta), path(hmmrank) ]

*.hmmrank.tsv.gz

`bai`

Channel containing subsets of sequences
Structure: [ val(meta), path(fasta) ]

*.fa.gz

`domain_summary`

Channel containing hmmsearch’s per-domain hit table, only present when save_domtblout is true
Structure: [ val(meta), path(domtbl) ]

*.domtbl.gz