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* Replace options.args3 with task.ext.args3 - 3 modules
* Replace options.args3 with task.ext.args3 - 17 modules
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Co-authored-by: JoseEspinosa <kadomu@gmail.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: MaxUlysse <max.u.garcia@gmail.com>
82 lines
2.2 KiB
YAML
82 lines
2.2 KiB
YAML
name: freebayes
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description: A haplotype-based variant detector
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keywords:
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- variant caller
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- SNP
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- genotyping
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- somatic variant calling
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- germline variant calling
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- bacterial variant calling
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- bayesian
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tools:
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- freebayes:
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description: Bayesian haplotype-based polymorphism discovery and genotyping
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homepage: https://github.com/freebayes/freebayes
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documentation: https://github.com/freebayes/freebayes
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tool_dev_url: https://github.com/freebayes/freebayes
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doi: "arXiv:1207.3907"
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licence: ['MIT']
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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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- input:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- input_index:
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type: file
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description: BAM/CRAM/SAM index file
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pattern: "*.bam.bai"
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- fasta:
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type: file
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description: reference fasta file
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pattern: ".{fa,fa.gz,fasta,fasta.gz}"
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- fasta_fai:
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type: file
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description: reference fasta file index
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pattern: "*.{fa,fasta}.fai"
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- targets:
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type: file
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description: Optional - Limit analysis to targets listed in this BED-format FILE.
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pattern: "*.bed"
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- samples:
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type: file
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description: Optional - Limit analysis to samples listed (one per line) in the FILE.
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pattern: "*.txt"
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- populations:
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type: file
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description: Optional - Each line of FILE should list a sample and a population which it is part of.
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pattern: "*.txt"
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- cnv:
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type: file
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description: |
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A copy number map BED file, which has either a sample-level ploidy:
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sample_name copy_number
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or a region-specific format:
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seq_name start end sample_name copy_number
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pattern: "*.bed"
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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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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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- vcf:
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type: file
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description: Compressed VCF file
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pattern: "*.vcf.gz"
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authors:
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- "@maxibor"
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- "@FriederikeHanssen"
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- "@maxulysse"
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