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08b71fa85f
* 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 * Add GUNC download_db and run commands * Bump with version without zgrep * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> * Harshil formatting * Apply suggestions from code review Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Maxime Borry <maxibor@users.noreply.github.com> Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
53 lines
1.5 KiB
YAML
53 lines
1.5 KiB
YAML
name: gunc_run
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description: Detection of Chimerism and Contamination in Prokaryotic Genomes
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keywords:
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- prokaryote
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- assembly
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- genome
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- quality control
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- chimeras
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tools:
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- gunc:
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description: Python package for detection of chimerism and contamination in prokaryotic genomes.
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homepage: https://grp-bork.embl-community.io/gunc/
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documentation: https://grp-bork.embl-community.io/gunc/
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tool_dev_url: https://github.com/grp-bork/gunc
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doi: "10.1186/s13059-021-02393-0"
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licence: ['GNU General Public v3 or later (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: FASTA file containing contig (bins)
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pattern: "*.fa"
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- db:
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type: file
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description: GUNC database file
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pattern: "*.dmnd"
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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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- maxcss_levels_tsv:
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type: file
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description: Output file with scores for a taxonomic level with the highest CSS score
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pattern: "*.tsv"
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- all_levels_tsv:
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type: file
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description: Optional output file with results for each taxonomic level
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pattern: "*.tsv"
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authors:
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- "@jfy133"
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