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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
50 lines
1.4 KiB
YAML
50 lines
1.4 KiB
YAML
name: ismapper
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description: Identify insertion sites positions in bacterial genomes
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keywords:
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- fastq
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- insertion sequences
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tools:
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- ismapper:
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description: A mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes.
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homepage: https://github.com/jhawkey/IS_mapper
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documentation: https://github.com/jhawkey/IS_mapper
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tool_dev_url: https://github.com/jhawkey/IS_mapper
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doi: "https://doi.org/10.1186/s12864-015-1860-2"
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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', single_end:false ]
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- reads:
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type: file
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description: A set of paired-end FASTQ files
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pattern: "*.{fastq.gz,fq.gz}"
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- reference:
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type: file
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description: Reference genome in GenBank format
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pattern: "*.{gbk}"
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- query:
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type: file
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description: Insertion sequences to query in FASTA format
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pattern: "*.{fasta,fa}"
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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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- results:
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type: directory
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description: Directory containing ISMapper result files
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pattern: "*/*"
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authors:
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- "@rpetit3"
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