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30b0485912
* Added support for meta in bwamem2/index * Added missing description of the input meta map (fasta file) * Made bwamem2/mem aware of the meta map the index carries * The output meta map needs to be same as the input bam file Don't merge it with the index's Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
54 lines
1.5 KiB
YAML
54 lines
1.5 KiB
YAML
name: bwamem2_mem
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description: Performs fastq alignment to a fasta reference using BWA
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keywords:
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- mem
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- bwa
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- alignment
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- map
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- fastq
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- bam
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- sam
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tools:
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- bwa:
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description: |
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BWA-mem2 is a software package for mapping DNA sequences against
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a large reference genome, such as the human genome.
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homepage: https://github.com/bwa-mem2/bwa-mem2
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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licence: ["MIT"]
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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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type: file
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description: BWA genome index files
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pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}"
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- sort_bam:
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type: boolean
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description: use samtools sort (true) or samtools view (false)
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pattern: "true or false"
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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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- 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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- "@maxulysse"
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