mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
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
|
|
description: Predict recomination events in bacterial genomes
|
|
keywords:
|
|
- fasta
|
|
- multiple sequence alignment
|
|
- recombination
|
|
tools:
|
|
- clonalframeml:
|
|
description: Efficient inferencing of recombination in bacterial genomes
|
|
homepage: https://github.com/xavierdidelot/ClonalFrameML
|
|
documentation: https://github.com/xavierdidelot/clonalframeml/wiki
|
|
tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML
|
|
doi: "10.1371/journal.pcbi.1004041"
|
|
licence: ["GPL v3"]
|
|
|
|
input:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- msa:
|
|
type: file
|
|
description: A multiple seqeunce alignmnet in FASTA format
|
|
pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
|
|
- newick:
|
|
type: file
|
|
description: A Newick formated tree based on multiple sequence alignment
|
|
pattern: "*.{newick,treefile,dnd}"
|
|
|
|
output:
|
|
- meta:
|
|
type: map
|
|
description: |
|
|
Groovy Map containing sample information
|
|
e.g. [ id:'test', single_end:false ]
|
|
- versions:
|
|
type: file
|
|
description: File containing software versions
|
|
pattern: "versions.yml"
|
|
- emsim:
|
|
type: file
|
|
description: Bootstrapped values for the three parameters R/theta, nu and delta
|
|
pattern: "*.emsim.txt"
|
|
- em:
|
|
type: file
|
|
description: Point estimates for R/theta, nu, delta and the branch lengths
|
|
pattern: "*.em.txt"
|
|
- fasta:
|
|
type: file
|
|
description: Sequence reconstructed by maximum likelihood
|
|
pattern: "*.ML_sequence.fasta"
|
|
- newick:
|
|
type: file
|
|
description: Tree with all nodes labelled
|
|
pattern: "*.labelled_tree.newick"
|
|
- pos_ref:
|
|
type: file
|
|
description: CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta
|
|
pattern: "*.position_cross_reference.txt"
|
|
- status:
|
|
type: file
|
|
description: List of reconstructed recombination events
|
|
pattern: "*.importation_status.txt"
|
|
|
|
authors:
|
|
- "@rpetit3"
|