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51 lines
1.5 KiB
YAML
51 lines
1.5 KiB
YAML
name: "snapaligner_align"
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description: Performs fastq alignment to a fasta reference using SNAP
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keywords:
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- alignment
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- map
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- fastq
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- bam
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- sam
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tools:
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- "snapaligner":
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description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data"
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homepage: "http://snap.cs.berkeley.edu"
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documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug"
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tool_dev_url: "https://github.com/amplab/snap"
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doi: "10.1101/2021.11.23.469039"
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licence: "['Apache v2']"
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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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- reads:
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type: file
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description: List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq
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pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}"
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- index:
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type: file
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description: List of SNAP genome index files
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pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}"
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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: Aligned BAM file
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pattern: "*.{bam}"
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- bai:
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type: file
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description: Optional aligned BAM file index
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pattern: "*.{bai}"
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authors:
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- "@matthdsm"
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