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nf-core_modules/modules/gatk4
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Praveen Raj S 68f1c27169
Changed tbi as optional output in GATK4 HaplotypeCaller (#1576) 
* Changed tbi as optional output. HC cannot index a VCF from large chromosomes.

* Apply suggestions from code review

* Update modules/gatk4/haplotypecaller/main.nf

Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-28 13:41:20 +02:00
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applybqsr Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
applybqsrspark Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
applyvqsr Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
baserecalibrator Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
baserecalibratorspark Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
bedtointervallist Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
calculatecontamination Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
combinegvcfs Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
createsequencedictionary Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
createsomaticpanelofnormals Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
estimatelibrarycomplexity Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
fastqtosam Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
filtermutectcalls Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
gatherbqsrreports Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
gatherpileupsummaries Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
genomicsdbimport Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
genotypegvcfs Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
getpileupsummaries Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
haplotypecaller Changed tbi as optional output in GATK4 HaplotypeCaller (#1576) 2022-04-28 13:41:20 +02:00
indexfeaturefile Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
intervallisttobed Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
intervallisttools Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
learnreadorientationmodel Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
markduplicates Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
markduplicatesspark typo in command line (#1523) 2022-04-13 15:15:44 +02:00
mergebamalignment Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
mergemutectstats Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
mergevcfs Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
mutect2 Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
revertsam Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
samtofastq Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
selectvariants Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
splitncigarreads add intervals possibilities to splitncigarreads (#1571) 2022-04-27 16:03:44 +02:00
variantfiltration Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
variantrecalibrator Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00