Maxime U. Garcia
eb15df8036
Deepvariant - Update main.nf ( #2110 )
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Update main.nf
simplify deepvariant container call
2022-09-27 15:34:10 +02:00
Ramprasad Neethiraj
fd5f6f5f4f
Revert recent changes made to some of the modules ( #1463 )
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* revert changes to modules
* fix tests
* fix kraken2
* fix untar
* fix cat
* add blank lines
* fix typo
2022-03-30 20:21:06 +02:00
Ramprasad Neethiraj
49b18b1639
add stub to modules used in raredisease pipeline ( #1206 )
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* add stub section
* add stub for bcftools norm
* add stub to more modules
* fix expansionhunter tests
* revert changes -picard
* Update stub to write version no.s to a file
* add picard
* revert picard again
* add stubs to more modules
* fix bwamem2
* add bcftools view
* add stubs
* fix svdb query
* review suggestions
2022-03-28 17:48:39 +02:00
FriederikeHanssen
c450b08a75
separate gvcf and vcf in output channels ( #1371 )
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* separate gvcf and vcf in output channels
* regex not working, just using prefix now
2022-03-03 11:54:07 +01:00
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
Mahesh Binzer-Panchal
e20e57f90b
Add when: block ( #1261 )
2022-02-04 09:53:32 +01:00
FriederikeHanssen
1287ba48fe
Update version & add intervals usage ( #1214 )
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* Update version & add intervals usage
* Fix config when passing intervals as file
* Use proper paths
2022-01-17 16:40:31 +01:00
Abhinav Sharma
6243c3792c
module: deepvariant ( #572 )
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* Add stubs for deepvariant [ci skip]
* Update the stubs for deepvariant [ci skip]
* functional with google docker image
* cleanup
* consume docker container within singularity executor
* update the meta.yml file and ask for review
* tweak the input channel shape and test data
* tweak input data [ci skip]
* update for the new syntax
* remove the functions and rename meta vars
* Update the arguments mechanism
* update chr, region and checksum
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-01-17 12:25:36 +02:00
