name: hmmer_hmmsearch description: search profile(s) against a sequence database keywords: - hidden Markov model - HMM - hmmer - hmmsearch tools: - hmmer: description: Biosequence analysis using profile hidden Markov models homepage: http://hmmer.org/ documentation: http://hmmer.org/documentation.html tool_dev_url: https://github.com/EddyRivasLab/hmmer doi: "10.1371/journal.pcbi.1002195" licence: ["BSD"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - hmmfile: type: file description: One or more HMM profiles created with hmmbuild pattern: "*.{hmm,hmm.gz}" - seqdb: type: file description: Database of sequences in FASTA format pattern: "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}" - write_align: type: val description: Flag to write optional alignment output. Specify with 'true' to output - write_target: type: val description: Flag to write optional per target summary . Specify with 'true' to output - write_domain: type: val description: Flag to write optional per domain summary. Specify with 'true' to output output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - output: type: file description: Human readable output summarizing hmmsearch results pattern: "*.{txt.gz}" - alignments: type: file description: Optional multiple sequence alignment (MSA) in Stockholm format pattern: "*.{sto.gz}" - target_summary: type: file description: Optional tabular (space-delimited) summary of per-target output pattern: "*.{tbl.gz}" - domain_summary: type: file description: Optional tabular (space-delimited) summary of per-domain output pattern: "*.{domtbl.gz}" authors: - "@Midnighter"