millironx/nf-core_modules
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nf-core_modules/modules/gatk4
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FriederikeHanssen 3df4fe6085
add freebayes/somatic and update freebayes/germline (#990) 
* add freebayes/somatic and update freebayes/germline to new syntax and cram

* add pytest

* update with new freebayes/germline path
2021-10-29 17:05:06 +02:00
..
applybqsr add freebayes/somatic and update freebayes/germline (#990) 2021-10-29 17:05:06 +02:00
baserecalibrator Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00
bedtointervallist Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
calculatecontamination Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
createsequencedictionary Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
createsomaticpanelofnormals Createsomaticpanelofnormals (#859) 2021-10-23 19:30:14 +01:00
estimatelibrarycomplexity Add gatk4/estimatelibrarycomplexity (#965) 2021-10-28 17:49:27 +02:00
fastqtosam Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
filtermutectcalls Filtermutectcalls (#796) 2021-10-23 18:45:19 +01:00
getpileupsummaries Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
haplotypecaller Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00
intervallisttools Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
learnreadorientationmodel Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
markduplicates Update to allow cram + update needed to use the gatk4 modules in sarek (#976) 2021-10-29 13:01:05 +02:00
mergebamalignment Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
mergevcfs Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
mutect2 Mutect2 add mitochondria mode and update tests (#967) 2021-10-29 11:27:56 +01:00
revertsam Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
samtofastq Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
splitncigarreads Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00
variantfiltration Backfill software licenses meta (#876) 2021-10-22 15:39:54 -07:00