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56 lines
1.5 KiB
YAML
56 lines
1.5 KiB
YAML
name: nextgenmap
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description: Performs fastq alignment to a fasta reference using NextGenMap
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keywords:
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- NextGenMap
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- ngm
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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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- bwa:
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description: |
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NextGenMap is a flexible highly sensitive short read mapping tool that
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handles much higher mismatch rates than comparable algorithms while
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still outperforming them in terms of runtime
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homepage: https://github.com/Cibiv/NextGenMap
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documentation: https://github.com/Cibiv/NextGenMap/wiki
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doi: 10.1093/bioinformatics/btt468
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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 FastQ files of size 1, if meta.single_end is true, and 2
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if meta.single_end is false.
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- fasta:
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type: file
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description: |
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Genomic reference fasta file
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pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}"
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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. First item of tuple with
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bam, below.
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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: |
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Output BAM file containing read alignments. Second item of tuple with
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meta, above
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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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- "@cmatkhan"
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