nf-core_modules/modules/hmmer/hmmsearch/meta.yml
Moritz E. Beber 938387d10d
feat: add hmmsearch module and tests (#1273)
* feat: add hmmsearch module and tests

* chore: set medium resource requirements

* tests: look for correct output

* fix: add when condition

* Apply suggestions to meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* refactor: create gzip compressed output

* docs: describe compressed in-/output

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-02-23 15:32:33 +01:00

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2.1 KiB
YAML

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"