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* saving changes to checkout * saving to sort out other branch * removed yml tracking of files that cant be tracked due to directory name changing between runs * test data added, ready for pr * fix eol linting error * Update modules/gatk4/genomicsdbimport/main.nf Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com> * merging with master * update push to show progress * tests now working untar able to pass data to genomicsdbimport * commit to checkout * tests updated, module reworked to simplify and emit updated gendb * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> * update meta.yml Priority of input options changed, updated to reflect this * Update test.yml name prefix changed in main script, test.yml updated to reflect this * fix tests due to review changes * bug fixes, multicalling samples and gendb emissions now fixed * Update pytest_modules.yml * Update meta.yml Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Francesco L <53608000+lescai@users.noreply.github.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> Co-authored-by: Gregor Sturm <mail@gregor-sturm.de> |
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| .. | ||
| applybqsr | ||
| baserecalibrator | ||
| bedtointervallist | ||
| calculatecontamination | ||
| createsequencedictionary | ||
| createsomaticpanelofnormals | ||
| estimatelibrarycomplexity | ||
| fastqtosam | ||
| filtermutectcalls | ||
| genomicsdbimport | ||
| getpileupsummaries | ||
| haplotypecaller | ||
| intervallisttools | ||
| learnreadorientationmodel | ||
| markduplicates | ||
| mergebamalignment | ||
| mergevcfs | ||
| mutect2 | ||
| revertsam | ||
| samtofastq | ||
| splitncigarreads | ||
| variantfiltration | ||