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* initial commit to setup branch * workflow finished * Update nextflow.config * tumour to tumor, getpileup passed as nomral and tumor * paired_somatic renamed to tumor_normal_somatic * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Update subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/main.nf Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * updated index names in meta.yml * changed index file names in main script and test * Apply suggestions from code review Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se> * Apply suggestions from code review * fixed bug from changes * Apply suggestions from code review * modified yml to allow new subworkflow testing * Update test.yml * Update test.yml * add applyvqsr * added memory options, new test data used * Update main.nf * Update main.nf Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
88 lines
3.1 KiB
YAML
88 lines
3.1 KiB
YAML
name: gatk4_applyvqsr
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description: |
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Apply a score cutoff to filter variants based on a recalibration table.
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AplyVQSR performs the second pass in a two-stage process called Variant Quality Score Recalibration (VQSR).
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Specifically, it applies filtering to the input variants based on the recalibration table produced
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in the first step by VariantRecalibrator and a target sensitivity value.
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keywords:
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- gatk4
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- applyvqsr
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- VQSR
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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']
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- vcf:
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type: file
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description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator.
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pattern: "*.vcf"
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- tbi:
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type: file
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description: Tbi index for the input vcf file.
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pattern: "*.vcf.tbi"
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- recal:
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type: file
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description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1.
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pattern: "*.recal"
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- recalidx:
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type: file
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description: Index file for the recalibration file.
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pattern: ".recal.idx"
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- tranches:
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type: boolean
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description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1.
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pattern: ".tranches"
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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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- allelespecific:
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type: boolean
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description: Whether or not to run ApplyVQSR in allele specific mode, this should be kept the same as the stage 1 VariantRecalibrator run.
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pattern: "{true,false}"
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- truthsensitivity:
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type: double
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description: Value to be used as the truth sensitivity cutoff score.
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pattern: "99.0"
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- mode:
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type: String
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description: Specifies which recalibration mode to employ, should be the same as the stage 1 VariantRecalibrator run. (SNP is default, BOTH is intended for testing only)
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pattern: "{SNP,INDEL,BOTH}"
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output:
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- vcf:
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type: file
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description: compressed vcf file containing the recalibrated variants.
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pattern: "*.vcf.gz"
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- tbi:
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type: file
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description: Index of recalibrated vcf file.
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pattern: "*vcf.gz.tbi"
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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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authors:
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- "@GCJMackenzie"
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