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a6e0629e24
* Change intervals to be part of sample specific input * Fix some tests * Update checksum * Update intervals * Update intervals * Try out gavins idea for adding the file * update test line * update test line * update test line * revert contains line
68 lines
1.9 KiB
YAML
68 lines
1.9 KiB
YAML
name: gatk4_applybqsr
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description: Apply base quality score recalibration (BQSR) to a bam file
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keywords:
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- bqsr
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- bam
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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/categories/360002369672s
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doi: 10.1158/1538-7445.AM2017-3590
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licence: ['Apache-2.0']
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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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- input:
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type: file
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description: BAM/CRAM file from alignment
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pattern: "*.{bam,cram}"
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- input_index:
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type: file
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description: BAI/CRAI file from alignment
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pattern: "*.{bai,crai}"
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- bqsr_table:
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type: file
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description: Recalibration table from gatk4_baserecalibrator
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- intervals:
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type: file
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description: Bed file with the genomic regions included in the library (optional)
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- fasta:
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type: file
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description: The reference fasta file
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pattern: "*.fasta"
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- fai:
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type: file
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description: Index of reference fasta file
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pattern: "*.fasta.fai"
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- dict:
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type: file
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description: GATK sequence dictionary
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pattern: "*.dict"
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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: Recalibrated BAM file
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pattern: "*.{bam}"
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authors:
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- "@yocra3"
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- "@FriederikeHanssen"
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