nf-core_modules/modules/ismapper/meta.yml

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name: ismapper
description: Identify insertion sites positions in bacterial genomes
keywords:
- fastq
- insertion sequences
tools:
- ismapper:
description: A mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes.
homepage: https://github.com/jhawkey/IS_mapper
documentation: https://github.com/jhawkey/IS_mapper
tool_dev_url: https://github.com/jhawkey/IS_mapper
doi: "https://doi.org/10.1186/s12864-015-1860-2"
licence: ["BSD-3-Clause"]
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- reads:
type: file
description: A set of paired-end FASTQ files
pattern: "*.{fastq.gz,fq.gz}"
- reference:
type: file
description: Reference genome in GenBank format
pattern: "*.{gbk}"
- query:
type: file
description: Insertion sequences to query in FASTA format
pattern: "*.{fasta,fa}"
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"
- results:
type: directory
description: Directory containing ISMapper result files
pattern: "*/*"
authors:
- "@rpetit3"