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90b203d3e9
* tool: elprep split * fixes for testing * fix tests * fix test outputs * create test-yaml * fix suggestions by @jfy133 Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
43 lines
1.2 KiB
YAML
43 lines
1.2 KiB
YAML
name: "elprep_split"
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description: Split bam file into manageable chunks
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keywords:
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- bam
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- split by chromosome
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tools:
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- "elprep":
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description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4."
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homepage: "https://github.com/ExaScience/elprep"
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documentation: "https://github.com/ExaScience/elprep"
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tool_dev_url: "https://github.com/ExaScience/elprep"
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doi: "10.1371"
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licence: "['AGPL 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: List of BAM/SAM files
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pattern: "*.{bam,sam}"
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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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#
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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: List of split BAM/SAM files
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pattern: "*.{bam,sam}"
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authors:
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- "@matthdsm"
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