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53 lines
1.4 KiB
YAML
53 lines
1.4 KiB
YAML
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name: samtools_bamtocram
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description: filter/convert and then index CRAM file
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keywords:
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- view
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- index
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- bam
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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/SAM file
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pattern: "*.{bam,sam}"
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- index:
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type: file
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description: BAM/SAM index file
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pattern: "*.{bai,sai}"
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- fasta:
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type: file
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description: Reference file to create the CRAM file
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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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- cram_crai:
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type: file
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description: filtered/converted CRAM file + index
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pattern: "*{.cram,.crai}"
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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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- "@FriederikeHanssen"
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- "@maxulysse"
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