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8bc5236371
* Created hmmer/eslalimask from template * esl-alimask module with --rf-is-mask test case * Add optional file output * Add hmmer to test name * Move from process_single to process_low * Test for versions.yml, plus content * Prettier * Avoid gzipping input alignment * hmmer/eslreformat from template * Started on main.nf * meta.id to prefix * Continued work * Fix version string so it's from *this* tool * hmmer/eslreformat * Prettier * Get tests/config/pytest_modules.yml back * Delete extra hmmer/eslalimask in pytest_modules.yml * More prettier * Fix path to versions.yml in test * Remove 'format' param * Fix problems with format param deletion * Document format param
41 lines
1.2 KiB
YAML
41 lines
1.2 KiB
YAML
name: "hmmer_eslreformat"
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description: reformats sequence files, see HMMER documentation for details. The module requires that the format is specified in ext.args in a config file, and that this comes last. See the tools help for possible values.
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keywords:
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- sort
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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: None
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doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195"
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licence: ["BSD-3-Clause"]
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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' ]
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- seqfile:
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type: file
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description: Sequences, aligned or not, in any supported format
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pattern: "*"
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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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- seqreformated:
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type: file
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description: Reformated sequence file
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pattern: "*.sequences.gz"
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authors:
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- "@erikrikarddaniel"
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