Description

search profile(s) against a sequence database

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

hmmfile (file)

One or more HMM profiles created with hmmbuild

*.{hmm,hmm.gz}

seqdb (file)

Database of sequences in FASTA format

*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}

write_align (val)

Flag to write optional alignment output. Specify with ‘true’ to output

write_target (val)

Flag to write optional per target summary . Specify with ‘true’ to output

write_domain (val)

Flag to write optional per domain summary. Specify with ‘true’ to output

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

output (file)

Human readable output summarizing hmmsearch results

*.{txt.gz}

alignments (file)

Optional multiple sequence alignment (MSA) in Stockholm format

*.{sto.gz}

target_summary (file)

Optional tabular (space-delimited) summary of per-target output

*.{tbl.gz}

domain_summary (file)

Optional tabular (space-delimited) summary of per-domain output

*.{domtbl.gz}
included in
funcscan metatdenovo
author
Github user Midnighter
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