millironx/nf-core_modules
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nf-core_modules/tests/modules/gatk4
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FriederikeHanssen e726b1730d
MD finally supports cram output (#2019) 
* MD finally supports cram output

* publish crai file

* fix test output

* fix mv

* figure out if contains breaks stuff

* remove variable checksum

* add contains check

* remove variable checksum

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-07 11:04:58 +02:00
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applybqsr Update md5sums 2022-05-12 16:07:12 +02:00
applybqsrspark remove variable checksum 2022-06-09 15:44:12 +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
calibratedragstrmodel add threads to calibratedragstrmodel 2022-06-07 12:11:18 +02:00
cnnscorevariants add brackets to contains 2022-05-23 13:19:42 +02:00
collectreadcounts new module gatk4/collectreadcounts (#1998) 2022-09-05 10:49:13 +02:00
combinegvcfs double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere 2022-05-12 16:16:53 +02:00
composestrtablefile linting 2022-06-01 09:20:20 +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
filtervarianttranches test path update 2022-05-23 12:53:36 +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 fix test input 2022-05-12 17:37:06 +02:00
getpileupsummaries getpileupsummaries requires intervals files 2022-05-12 16:51:17 +02:00
haplotypecaller Update tests/modules/gatk4/haplotypecaller/test.yml 2022-06-02 14:20:15 +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 Update md5sums 2022-05-12 16:07:12 +02:00
learnreadorientationmodel Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
leftalignandtrimvariants Add module: gatk4/leftalignandtrimvariants (#1808) 2022-06-28 10:44:08 +02:00
markduplicates MD finally supports cram output (#2019) 2022-09-07 11:04:58 +02:00
markduplicatesspark update checksum 2022-06-09 15:38:28 +02:00
mergebamalignment fix datatest for stubs 2022-05-06 15:34:18 +02:00
mergemutectstats Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
mergevcfs Updating test for gatk4/mergevcfs 2022-05-31 13:59:56 +00:00
mutect2 fix datatest for stubs 2022-05-06 15:34:18 +02:00
reblockgvcf fix test.yml 2022-06-09 15:14:37 +02:00
revertsam fix datatest for stubs 2022-05-06 15:34:18 +02:00
samtofastq fix datatest for stubs 2022-05-06 15:34:18 +02:00
selectvariants Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
splitintervals removed versions checksum 2022-05-13 14:27:59 +02:00
splitncigarreads Update md5sums 2022-05-12 16:07:12 +02:00
variantfiltration Improve syntax/logic coherence in all gatk4 plugins (#1459) 2022-04-12 17:15:39 +02:00
variantrecalibrator Variant recalibration (#1885) 2022-07-15 09:21:34 +02:00