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54e0ac4ed9
* committing to pull updated nf-core files * saving changes to checout other branch * committing progress so far, difficulty with test data * uploading to be used as draft PR * fix linting error in meta.yml * attempt to group reference inputs together * updated input format for resources * meta.yml updated with new resource names * added output channel for recal index * module only takes single vcf file input now * committing to checkout * update to new syntax, remove indel test for now * updated to use memory options and new test data * Update modules/gatk4/variantrecalibrator/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update main.nf * Update modules/gatk4/variantrecalibrator/main.nf Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * remove duplicate test keys from test_data.config Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> |
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| .. | ||
| applybqsr | ||
| applyvqsr | ||
| baserecalibrator | ||
| bedtointervallist | ||
| calculatecontamination | ||
| createsequencedictionary | ||
| createsomaticpanelofnormals | ||
| estimatelibrarycomplexity | ||
| fastqtosam | ||
| filtermutectcalls | ||
| gatherbqsrreports | ||
| genomicsdbimport | ||
| genotypegvcfs | ||
| getpileupsummaries | ||
| haplotypecaller | ||
| indexfeaturefile | ||
| intervallisttools | ||
| learnreadorientationmodel | ||
| markduplicates | ||
| mergebamalignment | ||
| mergevcfs | ||
| mutect2 | ||
| revertsam | ||
| samtofastq | ||
| splitncigarreads | ||
| variantfiltration | ||
| variantrecalibrator | ||