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54 lines
1.5 KiB
YAML
54 lines
1.5 KiB
YAML
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name: samtools_stats
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description: Produces comprehensive statistics from SAM/BAM/CRAM file
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keywords:
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- statistics
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- counts
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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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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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- input:
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type: file
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description: BAM/CRAM file from alignment
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pattern: "*.{bam,cram}"
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- input_index:
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type: file
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description: BAI/CRAI file from alignment
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pattern: "*.{bai,crai}"
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- fasta:
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type: optional file
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description: Reference file the CRAM was created with
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pattern: "*.{fasta,fa}"
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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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- stats:
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type: file
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description: File containing samtools stats output
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pattern: "*.{stats}"
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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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- "@drpatelh"
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- "@FriederikeHanssen"
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