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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>
58 lines
1.4 KiB
YAML
58 lines
1.4 KiB
YAML
name: methyldackel_extract
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description: Extracts per-base methylation metrics from alignments
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keywords:
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- methylation
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- 5mC
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- methylseq
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- bisulphite
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- consensus
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- bedGraph
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- bam
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- cram
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tools:
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- methyldackel:
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description: |
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A (mostly) universal methylation extractor
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for BS-seq experiments.
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homepage: https://github.com/brentp/bwa-meth
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documentation: https://github.com/brentp/bwa-meth
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arxiv: arXiv:1401.1129
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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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- fasta:
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type: file
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description: Input genome fasta file
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pattern: "*.{fasta,fa}"
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- fai:
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type: file
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description: FASTA index file
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pattern: "*.{fai}"
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- bam:
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type: file
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description: BAM/CRAM file
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pattern: "*.{bam,cram}"
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- bai:
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type: file
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description: BAM/CRAM index file
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pattern: "*.{bai,crai}"
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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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- bedgraph:
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type: file
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description: bedGraph file containing per-base methylation metrics
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pattern: "*.{bedGraph}"
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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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- "@phue"
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