mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 14:13:09 +00:00
03de60e6fa
* Bump checkM version and add support for pre-defined database * Add markfile output to checkm/lineagewf and add checkm/qa * Remove unnecessary BAM from tests * Fix channels to ensure single meta * Blah * Use secondary name evwyhere * Remove second incovcatiojn * Don't run module directrly for join * And for the other test * Correct module name * Fix name again * Try and fix out_format 9 not being picked up * Contains to matches to allow regex * Fix tests (finally) * Fix verisoning * [automated] Fix linting with Prettier * Update modules/checkm/qa/main.nf Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
67 lines
1.9 KiB
YAML
67 lines
1.9 KiB
YAML
name: checkm_qa
|
|
description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
|
|
keywords:
|
|
- checkm
|
|
- mag
|
|
- metagenome
|
|
- quality
|
|
- isolates
|
|
- microbes
|
|
- single cells
|
|
- completeness
|
|
- contamination
|
|
- bins
|
|
- genome bins
|
|
- qa
|
|
- quality assurnce
|
|
tools:
|
|
- checkm:
|
|
description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
|
|
homepage: https://ecogenomics.github.io/CheckM/
|
|
documentation: https://github.com/Ecogenomics/CheckM/wiki
|
|
tool_dev_url: https://github.com/Ecogenomics/CheckM
|
|
doi: "10.1101/gr.186072.114"
|
|
licence: ["GPL v3"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- analysis_dir:
|
|
type: file
|
|
description: Directory containing output of checkm/analyze or checkm/lineage_wf etc.
|
|
pattern: "*"
|
|
- marker_file:
|
|
type: file
|
|
description: Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf
|
|
pattern: "*.ms"
|
|
- coverage_file:
|
|
type: file
|
|
description: File containing coverage of each sequence (generated by checkm coverage)
|
|
- exclude_marker_file:
|
|
type: file
|
|
description: File specifying markers to exclude from marker sets
|
|
|
|
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: "Default completeness statistics in various formats, as specified with --out_format (excluding option: 9)"
|
|
pattern: "*.txt"
|
|
- fasta:
|
|
type: file
|
|
description: Output in fasta format (only if --out_format 9)
|
|
pattern: "*.fasta"
|
|
|
|
authors:
|
|
- "@jfy133"
|