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64 lines
1.7 KiB
YAML
64 lines
1.7 KiB
YAML
name: samtools_ampliconclip
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description: Clips read alignments where they match BED file defined regions
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keywords:
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- amplicon
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- clipping
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- ampliconclip
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- samtools
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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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- 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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- bed:
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type: file
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description: BED file of regions to be removed (e.g. amplicon primers)
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pattern: "*.{bed}"
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- save_cliprejects:
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type: value
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description: Save filtered reads to a file
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- save_clipstats:
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type: value
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description: Save clipping stats to a file
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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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- 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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- bam:
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type: file
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description: Clipped reads BAM file
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pattern: "*.{bam}"
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- stats:
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type: file
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description: Clipping statistics text file
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pattern: "*.{clipstats.txt}"
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- rejects_bam:
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type: file
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description: Filtered reads BAM file
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pattern: "*.{cliprejects.bam}"
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authors:
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- "@bjohnnyd"
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