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906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
52 lines
1.5 KiB
YAML
52 lines
1.5 KiB
YAML
name: subread_featurecounts
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description: Count reads that map to genomic features
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keywords:
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- counts
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- fasta
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- genome
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- reference
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tools:
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- featurecounts:
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description: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads.
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homepage: http://bioinf.wehi.edu.au/featureCounts/
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documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
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doi: "10.1093/bioinformatics/btt656"
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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: BAM/SAM file containing read alignments
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pattern: "*.{bam}"
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- annotation:
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type: file
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description: Genomic features annotation in GTF or SAF
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pattern: "*.{gtf,saf}"
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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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- counts:
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type: file
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description: Counts of reads mapping to features
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pattern: "*featureCounts.txt"
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- summary:
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type: file
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description: Summary log file
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pattern: "*.featureCounts.txt.summary"
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- version:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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authors:
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- "@ntoda03"
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