mirror of
https://github.com/MillironX/nf-core_modules.git
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e7845e2472
* msisensor2: Add msisensor2 module * msisensor2/scan module added * msisensor2 tests added Changes: - tests added for msisensor2 from the msisensor2 github repo. No available tests from NF-Core test repo. Relates to #1976 * msisensor2 slight bump in stuff * msisensor2: Replaced spelling of 'tumour' with 'tumor' * msisensor2: fix linting, testing and containers Relates to #1976 Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
59 lines
1.8 KiB
YAML
59 lines
1.8 KiB
YAML
name: "msisensor2_msi"
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description: msisensor2 detection of MSI regions.
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keywords:
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- msi
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tools:
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- "msisensor2":
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description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data."
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homepage: "https://github.com/niu-lab/msisensor2"
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documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md"
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tool_dev_url: "https://github.com/niu-lab/msisensor2"
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doi: ""
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licence: "GPL-3.0"
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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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#
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- tumor_bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- normal_bam:
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type: file
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description: BAM/CRAM/SAM file
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pattern: "*.{bam,cram,sam}"
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- intervals:
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type: file
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description: BED
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pattern: "*.bed"
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- models:
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type: file
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description: Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan)
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pattern: "*/*"
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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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- msi:
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type: file
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description: MSI classifications as a text file
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- distribution:
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type: file
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description: Read count distributions of MSI regions
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- somatic:
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type: file
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description: Somatic MSI regions detected.
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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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- "@adamrtalbot"
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