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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>
58 lines
1.9 KiB
YAML
58 lines
1.9 KiB
YAML
name: bamcmp
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description: Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX).
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keywords:
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- filter
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- xenograft
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- host
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- graft
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- contamination
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- mouse
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tools:
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- bamcmp:
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description:
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Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped,
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sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else
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reads which multimap to the contamination genome will be spuriously kept.
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homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp
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documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp
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tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp
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doi: "10.1158/1541-7786.MCR-16-0431"
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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']
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- sample:
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type: file
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description: BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep)
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pattern: "*.{bam,cram,sam}"
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- contaminant:
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type: file
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description: BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out)
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pattern: "*.{bam,cram,sam}"
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output:
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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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- bam:
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type: file
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description: Bam file containing the reads which align better to the primary genome.
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pattern: "*.{bam,cram,sam}"
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- bam:
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type: file
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description: Bam file containing the reads which align better to the contaminant genome.
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pattern: "*.{bam,cram,sam}"
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authors:
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- "@kmurat1"
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- "@sppearce"
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