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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
67 lines
2 KiB
YAML
67 lines
2 KiB
YAML
name: clonalframeml
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description: Predict recomination events in bacterial genomes
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keywords:
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- fasta
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- multiple sequence alignment
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- recombination
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tools:
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- clonalframeml:
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description: Efficient inferencing of recombination in bacterial genomes
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homepage: https://github.com/xavierdidelot/ClonalFrameML
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documentation: https://github.com/xavierdidelot/clonalframeml/wiki
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tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML
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doi: "10.1371/journal.pcbi.1004041"
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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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- msa:
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type: file
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description: A multiple seqeunce alignmnet in FASTA format
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pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
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- newick:
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type: file
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description: A Newick formated tree based on multiple sequence alignment
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pattern: "*.{newick,treefile,dnd}"
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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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- emsim:
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type: file
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description: Bootstrapped values for the three parameters R/theta, nu and delta
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pattern: "*.emsim.txt"
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- em:
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type: file
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description: Point estimates for R/theta, nu, delta and the branch lengths
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pattern: "*.em.txt"
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- fasta:
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type: file
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description: Sequence reconstructed by maximum likelihood
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pattern: "*.ML_sequence.fasta"
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- newick:
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type: file
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description: Tree with all nodes labelled
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pattern: "*.labelled_tree.newick"
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- pos_ref:
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type: file
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description: CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta
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pattern: "*.position_cross_reference.txt"
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- status:
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type: file
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description: List of reconstructed recombination events
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pattern: "*.importation_status.txt"
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authors:
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- "@rpetit3"
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