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66 lines
1.8 KiB
YAML
66 lines
1.8 KiB
YAML
name: minimap2_align
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description: A versatile pairwise aligner for genomic and spliced nucleotide sequences
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keywords:
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- align
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- fasta
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- fastq
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- genome
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- paf
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- reference
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tools:
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- minimap2:
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description: |
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A versatile pairwise aligner for genomic and spliced nucleotide sequences.
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homepage: https://github.com/lh3/minimap2
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documentation: https://github.com/lh3/minimap2#uguide
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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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- reads:
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type: file
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description: |
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List of input FASTA or FASTQ files of size 1 and 2 for single-end
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and paired-end data, respectively.
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- reference:
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type: file
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description: |
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Reference database in FASTA format.
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- bam_format:
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type: boolean
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description: Specify that output should be in BAM format
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- cigar_paf_format:
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type: boolean
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description: Specify that output CIGAR should be in PAF format
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- cigar_bam:
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type: boolean
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description: |
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Write CIGAR with >65535 ops at the CG tag. This is recommended when
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doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations)
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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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- paf:
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type: file
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description: Alignment in PAF format
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pattern: "*.paf"
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- bam:
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type: file
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description: Alignment in BAM format
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pattern: "*.bam"
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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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- "@heuermh"
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- "@sofstam"
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- "@sateeshperi"
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- "@jfy133"
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