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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> |
2 years ago | |
|---|---|---|
| .. | ||
| applybqsr | 2 years ago | |
| applybqsrspark | 2 years ago | |
| applyvqsr | 2 years ago | |
| baserecalibrator | 2 years ago | |
| baserecalibratorspark | 2 years ago | |
| bedtointervallist | 2 years ago | |
| calculatecontamination | 2 years ago | |
| calibratedragstrmodel | 2 years ago | |
| cnnscorevariants | 2 years ago | |
| collectreadcounts | 2 years ago | |
| collectsvevidence | 2 years ago | |
| combinegvcfs | 2 years ago | |
| composestrtablefile | 2 years ago | |
| createsequencedictionary | 2 years ago | |
| createsomaticpanelofnormals | 2 years ago | |
| estimatelibrarycomplexity | 2 years ago | |
| fastqtosam | 2 years ago | |
| filtermutectcalls | 2 years ago | |
| filtervarianttranches | 2 years ago | |
| gatherbqsrreports | 2 years ago | |
| gatherpileupsummaries | 2 years ago | |
| genomicsdbimport | 2 years ago | |
| genotypegvcfs | 2 years ago | |
| getpileupsummaries | 2 years ago | |
| haplotypecaller | 2 years ago | |
| indexfeaturefile | 2 years ago | |
| intervallisttobed | 2 years ago | |
| intervallisttools | 2 years ago | |
| learnreadorientationmodel | 2 years ago | |
| leftalignandtrimvariants | 2 years ago | |
| markduplicates | 2 years ago | |
| markduplicatesspark | 2 years ago | |
| mergebamalignment | 2 years ago | |
| mergemutectstats | 2 years ago | |
| mergevcfs | 2 years ago | |
| mutect2 | 2 years ago | |
| printsvevidence | 2 years ago | |
| reblockgvcf | 2 years ago | |
| revertsam | 2 years ago | |
| samtofastq | 2 years ago | |
| selectvariants | 2 years ago | |
| splitintervals | 2 years ago | |
| splitncigarreads | 2 years ago | |
| variantfiltration | 2 years ago | |
| variantrecalibrator | 2 years ago | |