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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>
54 lines
1.7 KiB
YAML
54 lines
1.7 KiB
YAML
name: mtnucratio
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description: A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file.
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keywords:
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- mtnucratio
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- ratio
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- reads
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- bam
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- mitochondrial to nuclear ratio
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- mitochondria
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- statistics
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tools:
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- mtnucratio:
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description: A small tool to determine MT to Nuclear ratios for NGS data.
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homepage: https://github.com/apeltzer/MTNucRatioCalculator
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documentation: https://github.com/apeltzer/MTNucRatioCalculator
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tool_dev_url: https://github.com/apeltzer/MTNucRatioCalculator
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doi: "10.1186/s13059-016-0918-z"
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licence: ["GPL v3"]
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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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- bam:
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type: file
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description: (coordinate) sorted BAM/SAM file
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pattern: "*.{bam,sam}"
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- mt_id:
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type: string
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description: Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria
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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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- mtnucratio:
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type: file
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description: Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio)
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pattern: "*.mtnucratio"
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- json:
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type: file
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description: JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file
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pattern: "*.json"
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authors:
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- "@louperelo"
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