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ac1e6df076
* Make samtools/merge cram compliant * samtools/stats cram compliance * update yml file * samtools/view to deal with crams * Update tests to make sure cram works * also fix tmp dir and min mem in one go * basequalityrecal test for cram + min mem + tmpdir * update haplotypecaller for sarek * update haplotype yml * update markdup to allow multiple bams, take out params to be passed with options.args * remove TODO statement * Remove variable md5sum * add emtpy input to stats module in subworkflows * subworkflows seem to work now on my side * Apply code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * replace bam with input to be more inclusive * rename everywhere * rename input * remove variable checksum Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
50 lines
1.6 KiB
YAML
50 lines
1.6 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: 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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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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- 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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