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* commit 08/07 * fixed formatting * atlas recal commit - corrected formatting * Fix tests * Fix meta.yml * Prettier * Delete nextflow * yaml > yml * Delete meta.yaml * Fix test * Forgot to run prettier? Co-authored-by: ltcrod <luca_traverso@kickseed.localdomain> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
58 lines
1.6 KiB
YAML
58 lines
1.6 KiB
YAML
name: "atlas_recal"
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description: gives an estimation of the sequencing bias based on known invariant sites
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keywords:
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- sequencing_bias
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- ATLAS
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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: "None"
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doi: "https://doi.org/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: BAM file
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pattern: "*.bam"
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- bai:
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type: file
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description: BAI file
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pattern: "*.bai"
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- empiric:
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type: file
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description: Optional txt file from PMD estimations (atlas/pmd)
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pattern: "*.txt"
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- alleles:
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type: file
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descrition: Optional bed file with known alleles
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pattern: "*.bed"
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- invariant_sites:
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type: file
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descrition: Optional bed file with invariant site coordinates
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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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- 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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- recal_patterns:
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type: file
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description: file containing the sequencing bias for each of the Read Group pools
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pattern: "*.txt"
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authors:
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- "@ltcrod"
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