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fead37d57a
* Add module: nf-core hackathon #207 : new module: msisensor/msi * Add module: nf-core hackathon #207 : new module: msisensor/msi * Fix 4-spacing issues (caught in PR linting) * Code review fixes & update configs * Code review: remove stray echo * Code review: Add msisensor modules * Slashes to underscores to get tests to run on github * Update software/msisensor/scan/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/msisensor/scan/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/msisensor/msi/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Update software/msisensor/msi/main.nf Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * Add all outputs to meta.ymls * Fixes from code review * Fixes from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
69 lines
2 KiB
YAML
69 lines
2 KiB
YAML
name: msisensor_msi
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description: Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data
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keywords:
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- homoploymer,microsatellite
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tools:
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- msisensor:
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description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline.
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homepage: https://github.com/ding-lab/msisensor
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documentation: None
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tool_dev_url: None
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doi: "10.1093/bioinformatics/btt755"
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licence: ['MIT']
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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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- normal_bam:
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type: file
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description: Coordinate sorted BAM/CRAM/SAM file from normal tissue
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pattern: "*.{bam,cram,sam}"
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- normal_bai:
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type: file
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description: Index for coordinate sorted BAM/CRAM/SAM file from normal tissue
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pattern: "*.{bam,cram,sam}"
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- tumor_bam:
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type: file
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description: Coordinate sorted BAM/CRAM/SAM file from tumor tissue
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pattern: "*.{bam,cram,sam}"
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- tumor_bai:
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type: file
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description: Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue
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pattern: "*.{bam,cram,sam}"
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- homopolymers:
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type: file
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description: Output file from MSIsensor scan module
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pattern: "*.msisensor_scan.tab"
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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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- 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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- txt:
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type: file
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description: MSIsensor MSI final report file
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pattern: "*.output"
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- txt:
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type: file
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description: MSIsensor MSI DIS report file
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pattern: "*.output_dis"
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- txt:
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type: file
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description: MSIsensor MSI germline report file
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pattern: "*.output_germline"
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- txt:
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type: file
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description: MSIsensor MSI somatic report file
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pattern: "*.output_somatic"
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authors:
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- "@kevbrick"
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