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4398056204
* Add tests and yml file for macs2/callpeak * add format option for macs2 * update macs2/callpeak to accept format argument * update test.yml * update the container version. * try to fix the issue in conda container. * Update conda and containers * Going back to previous container versions Co-authored-by: JoseEspinosa <kadomu@gmail.com>
63 lines
1.7 KiB
YAML
63 lines
1.7 KiB
YAML
name: macs2_callpeak
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description: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
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keywords:
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- alignment
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- atac-seq
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- chip-seq
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- peak-calling
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tools:
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- macs2:
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description: Model Based Analysis for ChIP-Seq data
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homepage: None
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documentation: https://docs.csc.fi/apps/macs2/
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tool_dev_url: https://github.com/macs3-project/MACS
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doi: "https://doi.org/10.1101/496521"
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licence: ['BSD']
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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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- ipbam:
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type: file
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description: The ChIP-seq treatment file
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- controlbam:
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type: file
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description: The control file
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- macs2_gsize:
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type: string
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description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9),
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'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)
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output:
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- versions:
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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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- peak:
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type: file
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description: BED file containing annotated peaks
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pattern: "*.gappedPeak,*.narrowPeak}"
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- xls:
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type: file
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description: xls file containing annotated peaks
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pattern: "*.xls"
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- gapped:
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type: file
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description: Optional BED file containing gapped peak
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pattern: "*.gappedPeak"
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- bed:
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type: file
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description: Optional BED file containing peak summits locations for every peak
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pattern: "*.bed"
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- bdg:
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type: file
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description: Optional bedGraph files for input and treatment input samples
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pattern: "*.bdg"
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authors:
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- "@ntoda03"
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- "@JoseEspinosa"
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- "@jianhong"
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