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nf-core_modules/modules/gatk4
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Lucpen f434d0c671
Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621) 
* 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>
2022-09-28 09:50:11 +02:00
..
applybqsr update gatk version 2022-05-12 15:45:21 +02:00
applybqsrspark similar issues arise with bqsrspark, also use broadinstitute container 2022-06-09 15:29:00 +02:00
applyvqsr update gatk version 2022-05-12 15:45:21 +02:00
baserecalibrator update gatk version 2022-05-12 15:45:21 +02:00
baserecalibratorspark similar issues arise with bqsrspark, also use broadinstitute container 2022-06-09 15:29:00 +02:00
bedtointervallist update gatk version 2022-05-12 15:45:21 +02:00
calculatecontamination update gatk version 2022-05-12 15:45:21 +02:00
calibratedragstrmodel changed to label to medium 2022-06-07 12:17:14 +02:00
cnnscorevariants remove variables used for test data generation, add tbi 2022-05-22 13:34:56 +02:00
collectreadcounts new module gatk4/collectreadcounts (#1998) 2022-09-05 10:49:13 +02:00
collectsvevidence new module gatk4/collectsvevidence (#2039) 2022-09-09 10:58:47 +02:00
combinegvcfs update gatk version 2022-05-12 15:45:21 +02:00
composestrtablefile spaces fix 2022-06-01 09:22:09 +02:00
createsequencedictionary update gatk version 2022-05-12 15:45:21 +02:00
createsomaticpanelofnormals update gatk version 2022-05-12 15:45:21 +02:00
estimatelibrarycomplexity update gatk version 2022-05-12 15:45:21 +02:00
fastqtosam update gatk version 2022-05-12 15:45:21 +02:00
filtermutectcalls Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621) 2022-09-28 09:50:11 +02:00
filtervarianttranches fix version 2022-05-23 12:15:33 +02:00
gatherbqsrreports Improve descriptions for modules with missing 2022-07-06 12:03:08 +02:00
gatherpileupsummaries update gatk version 2022-05-12 15:45:21 +02:00
genomicsdbimport update gatk version 2022-05-12 15:45:21 +02:00
genotypegvcfs update gatk version 2022-05-12 15:45:21 +02:00
getpileupsummaries GATK/Getpileupsummaries: If no intervals use variants instead (#1787) 2022-06-16 15:00:01 +02:00
haplotypecaller added dragstr model to haplotypecaller 2022-06-02 14:08:09 +02:00
indexfeaturefile update gatk version 2022-05-12 15:45:21 +02:00
intervallisttobed update gatk version 2022-05-12 15:45:21 +02:00
intervallisttools update gatk version 2022-05-12 15:45:21 +02:00
learnreadorientationmodel update gatk version 2022-05-12 15:45:21 +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 remove singulairty container 2022-06-09 15:16:11 +02:00
mergebamalignment update gatk version 2022-05-12 15:45:21 +02:00
mergemutectstats update gatk version 2022-05-12 15:45:21 +02:00
mergevcfs Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls (#1621) 2022-09-28 09:50:11 +02:00
mutect2 update gatk version 2022-05-12 15:45:21 +02:00
printsvevidence new module gatk4/printsvevidence (#2103) 2022-09-27 08:30:16 +02:00
reblockgvcf Update modules/gatk4/reblockgvcf/main.nf 2022-06-09 15:11:18 +02:00
revertsam update gatk version 2022-05-12 15:45:21 +02:00
samtofastq update gatk version 2022-05-12 15:45:21 +02:00
selectvariants update gatk version 2022-05-12 15:45:21 +02:00
splitintervals added tmp-dir + alignment correction 2022-05-13 14:35:22 +02:00
splitncigarreads update gatk version 2022-05-12 15:45:21 +02:00
variantfiltration update gatk version 2022-05-12 15:45:21 +02:00
variantrecalibrator Variant recalibration (#1885) 2022-07-15 09:21:34 +02:00