nf-core_modules/modules/atlas/recal/meta.yml

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name: "atlas_recal"
description: gives an estimation of the sequencing bias based on known invariant sites
keywords:
- sequencing_bias
- ATLAS
tools:
- "atlas":
description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity"
homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home"
tool_dev_url: "None"
doi: "https://doi.org/10.1101/105346"
licence: "['GPL v3']"
input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
- bam:
type: file
description: BAM file
pattern: "*.bam"
- bai:
type: file
description: BAI file
pattern: "*.bai"
- empiric:
type: file
description: Optional txt file from PMD estimations (atlas/pmd)
pattern: "*.txt"
- alleles:
type: file
descrition: Optional bed file with known alleles
pattern: "*.bed"
- invariant_sites:
type: file
descrition: Optional bed file with invariant site coordinates
pattern: "*.bed"
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"
- recal_patterns:
type: file
description: file containing the sequencing bias for each of the Read Group pools
pattern: "*.txt"
authors:
- "@ltcrod"