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
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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