2021-01-29 11:58:42 -05:00
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name: samtools_mpileup
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description: BAM
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keywords:
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- mpileup
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- bam
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- sam
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- cram
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tools:
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- samtools:
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description: |
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SAMtools is a set of utilities for interacting with and post-processing
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short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
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These files are generated as output by short read aligners like BWA.
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homepage: http://www.htslib.org/
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documentation: hhttp://www.htslib.org/doc/samtools.html
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doi: 10.1093/bioinformatics/btp352
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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: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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2021-01-29 13:12:17 -05:00
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- fasta:
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2021-01-29 11:58:42 -05:00
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type: file
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description: FASTA reference file
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2021-01-29 12:01:58 -05:00
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pattern: "*.{fasta,fa}"
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2021-01-29 11:58:42 -05:00
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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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- mpileup:
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type: file
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description: mpileup file
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pattern: "*.{mpileup}"
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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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- "@drpatelh"
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- "@joseespinosa"
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