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73 lines
2.2 KiB
YAML
73 lines
2.2 KiB
YAML
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name: "atlas_call"
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description: generate VCF file from a BAM file using various calling methods
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keywords:
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- atlas
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- variant calling
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- vcf
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- population genetics
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tools:
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- "atlas":
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description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
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homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
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documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
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tool_dev_url: "https://bitbucket.org/wegmannlab/atlas"
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doi: "10.1101/105346"
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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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- bam:
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type: file
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description: A BAM/ file
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pattern: "*.bam"
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- bai:
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type: file
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description: The BAI file for the input BAM file
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pattern: "*.bai"
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- fasta:
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type: file
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description: The reference FASTA file used to generate the BAM file
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pattern: "*.{fasta,fna,fa}"
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- fai:
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type: file
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description: The index of the FASTA file used for to generate the BAM file
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pattern: "*.fai"
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- recal:
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type: file
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description: Optional recalibration file from atlas recal function in text format
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pattern: "*.txt"
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- pmd:
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type: file
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description: Optional PMD file from atlas pmd function in text format
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pattern: "*.txt"
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- known_alleles:
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type: file
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description: Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation.
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pattern: "*.{txt.tsv}"
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- method:
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type: character
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description: Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation.
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pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase"
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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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- bam:
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type: file
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description: VCF file with variant calls
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pattern: "*.vcf.gz"
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authors:
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- "@jfy133"
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