name: gatk4_applybqsr description: Apply base quality score recalibration (BQSR) to a bam file keywords: - bqsr - bam tools: - gatk4: description: | Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - input: type: file description: BAM/CRAM file from alignment pattern: "*.{bam,cram}" - input_index: type: file description: BAI/CRAI file from alignment pattern: "*.{bai,crai}" - bqsr_table: type: file description: Recalibration table from gatk4_baserecalibrator - intervals: type: file description: Bed file with the genomic regions included in the library (optional) - fasta: type: file description: The reference fasta file pattern: "*.fasta" - fai: type: file description: Index of reference fasta file pattern: "*.fasta.fai" - dict: type: file description: GATK sequence dictionary pattern: "*.dict" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - bam: type: file description: Recalibrated BAM file pattern: "*.{bam}" authors: - "@yocra3" - "@FriederikeHanssen"