2021-02-17 17:23:11 +00:00
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name: bwameth_align
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description: Performs alignment of BS-Seq reads using bwameth
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keywords:
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- bwameth
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- alignment
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- 3-letter genome
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- map
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- fastq
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- bam
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tools:
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- bwameth:
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description: |
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Fast and accurate alignment of BS-Seq reads
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using bwa-mem and a 3-letter genome.
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homepage: https://github.com/brentp/bwa-meth
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documentation: https://github.com/brentp/bwa-meth
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arxiv: arXiv:1401.1129
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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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- reads:
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type: file
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description: |
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List of input FastQ files of size 1 and 2 for single-end and paired-end data,
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respectively.
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- index:
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2021-02-18 10:51:36 +00:00
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type: dir
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description: Directory containing bwameth genome index
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2021-02-17 17:23:11 +00:00
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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: Output BAM file containing read alignments
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pattern: "*.{bam}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@phue"
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