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* add qname feature to samtools_view * update tests * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/samtools/view/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * added filter tests Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
79 lines
2.2 KiB
YAML
79 lines
2.2 KiB
YAML
name: samtools_view
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description: filter/convert SAM/BAM/CRAM file
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keywords:
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- view
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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/SAM file
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pattern: "*.{bam,cram,sam}"
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- index:
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type: optional file
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description: BAM.BAI/CRAM.CRAI file
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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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- qname:
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type: file
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description: Optional file with read names to output only select alignments
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pattern: "*.{txt,list}"
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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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- bam:
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type: file
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description: optional filtered/converted BAM file
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pattern: "*.{bam}"
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- cram:
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type: file
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description: optional filtered/converted CRAM file
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pattern: "*.{cram}"
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- sam:
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type: file
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description: optional filtered/converted SAM file
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pattern: "*.{sam}"
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# bai, csi, and crai are created with `--write-index`
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- bai:
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type: file
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description: optional BAM file index
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pattern: "*.{bai}"
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- csi:
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type: file
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description: optional tabix BAM file index
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pattern: "*.{csi}"
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- crai:
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type: file
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description: optional CRAM file index
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pattern: "*.{crai}"
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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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- "@joseespinosa"
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- "@FriederikeHanssen"
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- "@priyanka-surana"
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