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f434d0c671
* feat added stubs to picard_liftovervcf * feat adding stubs to gatk4_mergevcfs * feat adding stubs to gatk4_filtermutectcalls * fix tests * fix output name filtermutectcalls * fix test * fix added missing [ * Update tests/modules/gatk4/mergevcfs/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update tests/modules/gatk4/filtermutectcalls/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update tests/modules/picard/liftovervcf/test.yml Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/filtermutectcalls/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/filtermutectcalls/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/mergevcfs/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/gatk4/mergevcfs/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Update modules/picard/liftovervcf/main.nf Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> * Trying something on picard_liftovervcf * fix adding test data for stubs * fix added bracket and unindented workflow * fix picard 2.27.1 -> 2.27.0 to solve PaddingError * Update main.nf fix added tbi to stub Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> |
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| .. | ||
| applybqsr | ||
| applybqsrspark | ||
| applyvqsr | ||
| baserecalibrator | ||
| baserecalibratorspark | ||
| bedtointervallist | ||
| calculatecontamination | ||
| calibratedragstrmodel | ||
| cnnscorevariants | ||
| collectreadcounts | ||
| collectsvevidence | ||
| combinegvcfs | ||
| composestrtablefile | ||
| createsequencedictionary | ||
| createsomaticpanelofnormals | ||
| estimatelibrarycomplexity | ||
| fastqtosam | ||
| filtermutectcalls | ||
| filtervarianttranches | ||
| gatherbqsrreports | ||
| gatherpileupsummaries | ||
| genomicsdbimport | ||
| genotypegvcfs | ||
| getpileupsummaries | ||
| haplotypecaller | ||
| indexfeaturefile | ||
| intervallisttobed | ||
| intervallisttools | ||
| learnreadorientationmodel | ||
| leftalignandtrimvariants | ||
| markduplicates | ||
| markduplicatesspark | ||
| mergebamalignment | ||
| mergemutectstats | ||
| mergevcfs | ||
| mutect2 | ||
| printsvevidence | ||
| reblockgvcf | ||
| revertsam | ||
| samtofastq | ||
| selectvariants | ||
| splitintervals | ||
| splitncigarreads | ||
| variantfiltration | ||
| variantrecalibrator | ||