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a740a6ff48
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * feat: add megahit module, currently decompressed output * Update main.nf * Update tests/modules/megahit/test.yml Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * feat: compress all outputs, remove md5sums due to gz stochasicity * fix: wrong conda channel for pigz * fix: broken singleend tests and update meta.yml * Missed one * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * fix: pigz formatting * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Apply suggestions from code review * Added but test failing due to null on output channel * fix prefix variable * Complete checkm_lineagewf * Remove TODOs * Add description of fasta_ext parameter * Improve meta map for this context * Update meta.yml * Update modules/checkm/lineagewf/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
58 lines
1.6 KiB
YAML
58 lines
1.6 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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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_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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