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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>
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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- 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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- "@ntoda03"
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