2020-08-07 08:24:24 -04:00
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name: bwa_mem
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description: Performs fastq alignment to a fasta reference using BWA
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2020-08-05 12:27:42 -04:00
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keywords:
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2020-08-07 10:05:25 -04:00
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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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2020-08-05 12:27:42 -04:00
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tools:
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2020-08-07 10:05:25 -04:00
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- bwa:
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description: |
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BWA 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: http://bio-bwa.sourceforge.net/
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documentation: http://www.htslib.org/doc/samtools.html
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arxiv: arXiv:1303.3997
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2020-08-05 12:27:42 -04:00
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input:
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2020-08-07 10:05:25 -04:00
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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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2021-02-02 07:34:55 -05:00
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pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}"
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2020-08-05 12:27:42 -04:00
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output:
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2020-08-07 10:05:25 -04:00
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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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2020-08-05 12:27:42 -04:00
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authors:
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2020-08-07 10:05:25 -04:00
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- "@drpatelh"
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- "@jeremy1805"
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