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e726b1730d
* MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
72 lines
2.1 KiB
YAML
72 lines
2.1 KiB
YAML
name: gatk4_markduplicates
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description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
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keywords:
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- markduplicates
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- bam
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- sort
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tools:
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- gatk4:
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description:
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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools
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with a primary focus on variant discovery and genotyping. Its powerful processing engine
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and high-performance computing features make it capable of taking on projects of any size.
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homepage: https://gatk.broadinstitute.org/hc/en-us
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documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard-
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tool_dev_url: https://github.com/broadinstitute/gatk
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doi: 10.1158/1538-7445.AM2017-3590
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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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- bam:
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type: file
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description: Sorted BAM file
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pattern: "*.{bam}"
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- fasta:
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type: file
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description: Fasta file
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pattern: "*.{fasta}"
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- fasta_fai:
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type: file
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description: Fasta index file
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pattern: "*.{fai}"
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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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- 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: Marked duplicates BAM file
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pattern: "*.{bam}"
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- cram:
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type: file
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description: Marked duplicates CRAM file
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pattern: "*.{cram}"
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- bai:
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type: file
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description: BAM index file
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pattern: "*.{bam.bai}"
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- crai:
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type: file
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description: CRAM index file
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pattern: "*.{cram.crai}"
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- metrics:
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type: file
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description: Duplicate metrics file generated by GATK
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pattern: "*.{metrics.txt}"
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authors:
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- "@ajodeh-juma"
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- "@FriederikeHanssen"
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- "@maxulysse"
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