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53 lines
1.4 KiB
YAML
53 lines
1.4 KiB
YAML
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name: biobambam_bamsormadup
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description: Parallel sorting and duplicate marking
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keywords:
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- markduplicates
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- sort
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- bam
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- cram
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tools:
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- biobambam:
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description: |
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biobambam is a set of tools for early stage alignment file processing.
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homepage: https://gitlab.com/german.tischler/biobambam2
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documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md
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doi: 10.1186/1751-0473-9-13
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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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- bams:
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type: file
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description: List containing 1 or more bam files
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- fasta:
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type: file
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description: Reference genome in FASTA format (optional)
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pattern: "*.{fa,fasta}"
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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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- bam:
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type: file
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description: BAM/CRAM file with duplicate reads marked/removed
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pattern: "*.{bam,cram}"
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- bam_index:
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type: file
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description: BAM index file
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pattern: "*.{bai}"
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- metrics:
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type: file
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description: Duplicate metrics file generated by biobambam
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pattern: "*.{metrics.txt}"
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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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authors:
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- "@matthdsm"
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