Rike
169b2b96c1
update gatk version
2022-05-12 15:45:21 +02:00
Maxime U. Garcia
409af2f27c
Improve syntax/logic coherence in all gatk4 plugins ( #1459 )
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* feat: code polishing
* Apply suggestions from code review
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* code polishing
* more code polishing
* code polishing
* tests for applybqsrspark
* fix typo
* no need to check md5sum for versions.yml
* fix: use correct syntax
* code polishing again
* add tests for markduplicatesspark
* simplify mergevcfs tests
* add tests for baserecalibratorspark
* fix: path to entry
* code polishing
* fix linting
* simplify module
* update meta.yml
* fix pair mode
* fix: MITO mode
* more tests
* fix command
* bad copy paste
* fix typos
* fix tests
* fix test
* update meta.yml
* correct versions.yml in all test.yml
* code polishing
* code polishing
* more code polishing
* fix args
* add tmpdir for all
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 17:15:39 +02:00
Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config ( #1279 )
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* fix yml formatting
* allow fastq.gz and fq.gz as file input, add meta.yml and test
* fix yaml files
* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"
This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.
* prettier magic!
* fix comments for yamllint
* remove node version number
* fix linting errors
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
FriederikeHanssen
967fb22ded
Update versions ( #1292 )
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* Update versions
* update checksums + remove variables as input for applyvqsr
* sneak in removal of values and provide them via modules.config
* update another checksum
* more checksums
* move vairable to config
* remove controlfreec, wrong branch
* add line break
2022-02-15 11:29:36 +01:00
Mahesh Binzer-Panchal
e20e57f90b
Add when: block ( #1261 )
2022-02-04 09:53:32 +01:00
FriederikeHanssen
598d7abdb2
Log4j again ( #1202 )
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* Log4j again
* Update checksums
2022-01-12 13:55:54 +01:00
FriederikeHanssen
50eafb19c6
Update version for log4j vulnerability ( #1176 )
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* Update version for log4j vulnerability
* update checksums
* update checksums
* update checksums
* Remove todo string
* remove werid output paths
* remove werid output paths
* remove werid output paths
* Update various checksums
* Update various checksums
* Remove unstable md5sums
* Update md5sums
* Fix pileupsummary
* Fix genotypegvcfs
* Update test files mutect2
* hm genotypevcf updated again
* Update some mutect checksums and whatnot
* Fix last mutect checksum
* Apply suggestion to use mtochondria data instead
2021-12-20 17:10:49 +01:00
FriederikeHanssen
a9dd46f010
add gatk4/gatherbqsr ( #1130 )
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* nf-core modules create
* add module files
* indent
* remove templte code
* manually revert pytest changes from tools
* manually revert pytest changes from tools
* add include statement back in
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2021-12-08 23:43:36 +01:00
