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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>
65 lines
1.8 KiB
YAML
65 lines
1.8 KiB
YAML
name: checkm_lineagewf
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description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
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keywords:
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- checkm
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- mag
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- metagenome
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- quality
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- isolates
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- microbes
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- single cells
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- completeness
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- contamination
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- bins
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- genome bins
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tools:
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- checkm:
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description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
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homepage: https://ecogenomics.github.io/CheckM/
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documentation: https://github.com/Ecogenomics/CheckM/wiki
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tool_dev_url: https://github.com/Ecogenomics/CheckM
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doi: "10.1101/gr.186072.114"
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licence: ["GPL v3"]
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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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- fasta:
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type: file
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description: One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value
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pattern: "*.{$fasta_ext}"
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- fasta_ext:
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type: value
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description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas)
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- db:
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type: directory
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description: Optional directory pointing to checkM database to prevent re-downloading
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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:'sample', bin:'1' ]
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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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- checkm_output:
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type: directory
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description: CheckM output directory
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pattern: "*/"
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- checkm_output:
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type: file
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description: Lineage markfer file
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pattern: "lineage.ms"
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- checkm_tsv:
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type: file
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description: CheckM summary completeness statistics table
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pattern: "*.tsv"
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authors:
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- "@jfy133"
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