search profile(s) against a sequence database
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
hmmfile
:file
One or more HMM profiles created with hmmbuild
*.{hmm,hmm.gz}
seqdb
Database of sequences in FASTA format
*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}
write_align
:boolean
Flag to save optional alignment output. Specify with ‘true’ to save.
write_target
Flag to save optional per target summary. Specify with ‘true’ to save.
write_domain
Flag to save optional per domain summary. Specify with ‘true’ to save.
output
*.txt.gz
Human readable output summarizing hmmsearch results
*.{txt.gz}
alignments
*.sto.gz
Optional multiple sequence alignment (MSA) in Stockholm format
*.{sto.gz}
target_summary
*.tbl.gz
Optional tabular (space-delimited) summary of per-target output
*.{tbl.gz}
domain_summary
*.domtbl.gz
Optional tabular (space-delimited) summary of per-domain output
*.{domtbl.gz}
versions_hmmer
${task.process}
:string
The name of the process
hmmer
The name of the tool
hmmsearch -h | sed '2!d;s/^# HMMER *//;s/ .*//'
:eval
The expression to obtain the version of the tool
versions
Biosequence analysis using profile hidden Markov models
