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nf-core_modules/tests/modules/gatk4
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James A. Fellows Yates e080f4c8ac
Untar unzip meta (#1408) 
* fix: remove left-over unnecessary code

* Adds support for meta lists for unzip and untar

* Fix test inputs

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple

* Fix MALTEXTRACT/AMPS

* Fix further modules

* Fix cellranger

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-03-21 14:49:28 +01:00
..
applybqsr Update versions (#1292) 2022-02-15 11:29:36 +01:00
applyvqsr Update versions (#1292) 2022-02-15 11:29:36 +01:00
baserecalibrator Change intervals to be part of sample specific input (#1189) 2021-12-23 12:58:20 +01:00
bedtointervallist Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
calculatecontamination Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
combinegvcfs Prettier (#1405) 2022-03-18 14:27:50 +01:00
createsequencedictionary Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
createsomaticpanelofnormals Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
estimatelibrarycomplexity Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
fastqtosam Update versions (#1292) 2022-02-15 11:29:36 +01:00
filtermutectcalls Update version for log4j vulnerability (#1176) 2021-12-20 17:10:49 +01:00
gatherbqsrreports Update versions (#1292) 2022-02-15 11:29:36 +01:00
gatherpileupsummaries Add gatherpileupsummaries (#1311) 2022-02-17 15:05:21 +01:00
genomicsdbimport Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
genotypegvcfs Untar unzip meta (#1408) 2022-03-21 14:49:28 +01:00
getpileupsummaries Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
haplotypecaller Change intervals to be part of sample specific input (#1189) 2021-12-23 12:58:20 +01:00
indexfeaturefile Update versions (#1292) 2022-02-15 11:29:36 +01:00
intervallisttobed intervallisttobed (#1312) 2022-02-17 16:32:26 +01:00
intervallisttools Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
learnreadorientationmodel Change syntax from task.ext.suffix to tast.ext.prefix in all modules (#1110) 2021-12-02 12:39:55 +00:00
markduplicates Update versions (#1292) 2022-02-15 11:29:36 +01:00
mergebamalignment Update mergebam syntax and sample specific unmapped channel (#1238) 2022-01-27 15:30:27 +00:00
mergemutectstats add mergemutectstats (#1314) 2022-02-18 09:38:55 +01:00
mergevcfs Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
mutect2 Update intervals (#1278) 2022-02-10 10:34:22 +01:00
revertsam Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
samtofastq Update all modules to new NF DSL2 syntax (#1099) 2021-11-26 07:58:40 +00:00
selectvariants Gatk4 selectvariants (#1346) 2022-02-24 09:51:48 +01:00
splitncigarreads Update versions (#1292) 2022-02-15 11:29:36 +01:00
variantfiltration Fix formatting in yaml files, add yamllint config (#1279) 2022-02-15 11:15:27 +00:00
variantrecalibrator Update versions (#1292) 2022-02-15 11:29:36 +01:00