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