Adam Talbot 009f7c691c Add module: gatk4/leftalignandtrimvariants (#1808) ... * Added: gatk4/leftalignandtrimvariants Additions: - GATK4/LeftAlignAndTrimVariants module - Use sars-ncov2 test data as this normalises a larger INDEL correctly. Fixes #1801 * fixup: Added index to output spec * fixup: Pattern of tbi output corrected to 'tbi' * gatk4/leftalignandtrimvariants: Added intervals Changes: - gatk4/leftalignandtrimvariants now supports optional interval as BED file - Tests added with and without interval. Not test BED file excludes all variants so no variants are actually normalised. Fixes #1801 * fixup: leftalignandtrimvariants vcf->tbi fix * fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml		2022-06-28 10:44:08 +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
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	update gatk version	2022-05-12 15:45:21 +02:00
filtervarianttranches	fix version	2022-05-23 12:15:33 +02:00
gatherbqsrreports	update gatk version	2022-05-12 15:45:21 +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	Merge branch 'master' into process_lable_markdup	2022-05-16 15:53:26 +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	Removing redundant empty line	2022-05-31 15:34:34 +00:00
mutect2	update gatk version	2022-05-12 15:45:21 +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	update gatk version	2022-05-12 15:45:21 +02:00