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e745e167c1
* fix yml formatting * allow fastq.gz and fq.gz as file input, add meta.yml and test * fix yaml files * Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test" This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4. * prettier magic! * fix comments for yamllint * remove node version number * fix linting errors Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
50 lines
1.4 KiB
YAML
50 lines
1.4 KiB
YAML
name: nucmer
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description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.
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keywords:
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- align
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- nucleotide
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tools:
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- nucmer:
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description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences.
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homepage: http://mummer.sourceforge.net/
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documentation: http://mummer.sourceforge.net/
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tool_dev_url: http://mummer.sourceforge.net/
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doi: "https://doi.org/10.1186/gb-2004-5-2-r12"
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licence: ["The Artistic License"]
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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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- ref:
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type: file
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description: FASTA file of the reference sequence
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pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}"
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- query:
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type: file
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description: FASTA file of the query sequence
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pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.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
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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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- delta:
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type: file
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description: File containing coordinates of matches between reference and query
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- coords:
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type: file
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description: NUCmer1.1 coords output file
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pattern: "*.{coords}"
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authors:
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- "@sateeshperi"
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- "@mjcipriano"
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