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* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Start work, continue once on non-mobile internet * finished and working on conda * Update modules/amps/main.nf Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> * Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com> Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
66 lines
1.8 KiB
YAML
66 lines
1.8 KiB
YAML
name: amps
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description: Post-processing script of the MaltExtract component of the HOPS package
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keywords:
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- malt
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- MaltExtract
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- HOPS
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- amps
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- alignment
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- metagenomics
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- ancient DNA
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- aDNA
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- palaeogenomics
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- archaeogenomics
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- microbiome
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- authentication
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- damage
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- edit distance
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- post Post-processing
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- visualisation
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tools:
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- amps:
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description: Post-processing script of the MaltExtract tool for ancient metagenomics
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homepage: "https://github.com/rhuebler/HOPS"
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documentation: "https://github.com/keyfm/amps"
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tool_dev_url: "https://github.com/keyfm/amps"
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doi: "10.1186/s13059-019-1903-0"
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licence: ['GPL >=3']
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input:
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- maltextract_results:
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type: directory
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description: MaltExtract output directory
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pattern: "results/"
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- taxon_list:
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type: file
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description: List of target taxa to evaluate used in MaltExtract
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pattern: "*.txt"
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- filter:
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type: string
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description: The filter mode used in MaltExtract
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pattern: "def_anc|default|scan|ancient|crawl"
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output:
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- version:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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- json:
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type: file
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description: Candidate summary heatmap in MultiQC compatible JSON format
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pattern: "heatmap_overview_Wevid.json"
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- summary_pdf:
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type: file
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description: Candidate summary heatmap in PDF format
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pattern: "heatmap_overview_Wevid.pdf"
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- tsv:
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type: file
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description: Candidate summary heatmap in TSV format
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pattern: "heatmap_overview_Wevid.tsv"
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- candidate_pdfs:
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type: directory
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description: Directory of per sample output PDFs organised by reference
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pattern: "pdf_candidate_profiles/"
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authors:
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- "@jfy133"
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