millironx/nf-core_modules
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nf-core_modules/modules/gatk4
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Maxime U. Garcia 409af2f27c
Improve syntax/logic coherence in all gatk4 plugins (#1459) 
* feat: code polishing

* Apply suggestions from code review

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>

* code polishing

* more code polishing

* code polishing

* tests for applybqsrspark

* fix typo

* no need to check md5sum for versions.yml

* fix: use correct syntax

* code polishing again

* add tests for markduplicatesspark

* simplify mergevcfs tests

* add tests for baserecalibratorspark

* fix: path to entry

* code polishing

* fix linting

* simplify module

* update meta.yml

* fix pair mode

* fix: MITO mode

* more tests

* fix command

* bad copy paste

* fix typos

* fix tests

* fix test

* update meta.yml

* correct versions.yml in all test.yml

* code polishing

* code polishing

* more code polishing

* fix args

* add tmpdir for all

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 17:15:39 +02:00
..
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 Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +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 Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +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 Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +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