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* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
52 lines
1.6 KiB
YAML
52 lines
1.6 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: "*.{version.txt}"
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authors:
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- "@ntoda03"
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