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nf-core_modules/modules/gatk4
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Sateesh a25423dbb9
Gatk4 combinegvcfs (#1342) 
* add gatk4/combinegvcfs module

* update gatk4/combinegvcfs

* loop to create a string adding -V to each vcf file

* add contains for variable md5

* rm whitespace

* meta in output

* fix indentations

* fix indentations

* move tmpdir to args and update conda version

Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-23 16:29:29 +01:00
..
applybqsr Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
applyvqsr Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
baserecalibrator Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
bedtointervallist Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
calculatecontamination Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
combinegvcfs Gatk4 combinegvcfs (#1342) 2022-02-23 16:29:29 +01:00
createsequencedictionary Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
createsomaticpanelofnormals Update versions (#1292) 2022-02-15 11:29:36 +01:00
estimatelibrarycomplexity Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
fastqtosam Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
filtermutectcalls Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gatherbqsrreports Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
gatherpileupsummaries Add gatherpileupsummaries (#1311) 2022-02-17 15:05:21 +01:00
genomicsdbimport Update versions (#1292) 2022-02-15 11:29:36 +01:00
genotypegvcfs update priority (#1334) 2022-02-22 14:25:36 +01:00
getpileupsummaries Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
haplotypecaller Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
indexfeaturefile Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
intervallisttobed intervallisttobed (#1312) 2022-02-17 16:32:26 +01:00
intervallisttools Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
learnreadorientationmodel Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
markduplicates Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mergebamalignment Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mergemutectstats add mergemutectstats (#1314) 2022-02-18 09:38:55 +01:00
mergevcfs Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
mutect2 Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
revertsam Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
samtofastq Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
splitncigarreads Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
variantfiltration Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
variantrecalibrator Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00