FriederikeHanssen
1ac223ad43
GATK/Getpileupsummaries: If no intervals use variants instead ( #1787 )
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If no intervals use variants instead
2022-06-16 15:00:01 +02:00
Matthias De Smet
ecece498f1
samtools/*stats*: use prefix for outputs ( #1788 )
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* use prefix in flagstat
* use prefix in idxstats
* use prefix in stats
* update test.yml
2022-06-16 13:42:01 +02:00
Robert A. Petit III
052b9f2fe9
add module for plasmidfinder ( #1773 )
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* add module for plasmidfinder
* Update test.yml
2022-06-15 10:25:51 -06:00
Robert A. Petit III
1fe4cb942f
add module for ariba ( #1731 )
2022-06-15 10:18:31 -06:00
Anders Sune Pedersen
30f72e2482
Optional output from the VEP-moduel ( #1775 )
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* Making the output from the VEP-moduel (ENSEMBLVEP) optionally vcf, json or tab. #1774
* Trying to fix tests
* Still trying to fix tests
* Fetching the vep-output-file-extension from the args.
* Update meta.yml
* WIP: Adding tests for vep-output json and tab
* updated the test.yml
Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Co-authored-by: nvnieuwk <nicolas.vannieuwkerke@ugent.be>
2022-06-15 13:52:12 +02:00
nvnieuwk
9dbaffff88
fix bgziptabix extension ( #1784 )
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* fix bgziptabix extension
* update test.yml
2022-06-15 10:33:10 +02:00
Mahesh Binzer-Panchal
0af6adef55
Add MerquryFK PloidyPlot ( #1780 )
2022-06-14 20:50:58 +02:00
Mahesh Binzer-Panchal
e91e99db30
Add GeneScopeFK ( #1781 )
2022-06-14 20:49:06 +02:00
Mahesh Binzer-Panchal
8ded6d441a
Add MerquryFK ( #1778 )
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* Add MerquryFK
* Change resource allocation
2022-06-14 16:36:02 +02:00
Mahesh Binzer-Panchal
fd5aea0b76
Add FastK/Histex ( #1776 )
2022-06-14 16:30:37 +02:00
nvnieuwk
1a4ab76618
new module rtgtools/pedfilter ( #1777 )
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* new module rtgtools/pedfilter
* removed checksum due to the presence of a date in the file
2022-06-14 16:02:18 +02:00
Mahesh Binzer-Panchal
4e308c131e
FastK/fastK ( #1739 )
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* Add FastK/FastK
* Add ktab and prof outputs
* Add the hidden files necessary for the optional files
* Update image
* Apply suggestions from code review
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-06-14 13:39:52 +02:00
8b2a473f58
New module: krakentools/kreport2krona ( #1746 )
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* Add module definition for kreport2krona
* Add metadata for kreport2krona module
* Add tests for kreport2krona
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-06-13 20:14:44 +02:00
Maxime U. Garcia
b689b8ed88
TIDDIT - add --skip_assembly when no bwa specified ( #1769 )
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add --skip_assembly when no bwa specified
2022-06-13 17:02:59 +02:00
Maxime U. Garcia
680b6c5b04
Update tiddit to 3.1.0 ( #1767 )
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* update TIDDIT to 3.1.0
* update VCF too as version is in file
2022-06-13 16:24:34 +02:00
Merlin Szymanski
8f199c4fa4
Create atlas/splitmerge Module ( #1756 )
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* Add atlas/splitmerge module
* Finish the tests for atlas/splitmerge
* Prettier
* Update modules/atlas/splitmerge/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Remove curly brackets from meta.yml parameters
For single-file outputs, as reviewed
* Lintung: Remove trailing white-space
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-13 15:09:32 +02:00
Robert A. Petit III
81232af296
add module for mcroni ( #1750 )
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Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-06-13 15:04:01 +02:00
WackerO
f1b3174501
Merge branch 'master' into mpileup_bgzip
2022-06-13 09:48:47 +02:00
WackerO
24e05f6097
Update modules/samtools/mpileup/main.nf
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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-06-13 09:35:34 +02:00
FriederikeHanssen
5b27af025a
Merge branch 'master' into manta_convert
2022-06-13 09:29:50 +02:00
FriederikeHanssen
b8ff8e32e3
Update modules/manta/convertinversion/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-13 09:26:29 +02:00
WackerO
c3b6ec8f3b
Merge branch 'master' of https://github.com/nf-core/modules into mpileup_bgzip
2022-06-13 08:31:01 +02:00
WackerO
dc6c09e083
samtools mpileup now bgzips mpileup files
2022-06-11 13:32:53 +02:00
Rike
dd6c514710
Fix linting
2022-06-11 13:12:56 +02:00
Rike
650076cacf
add manta conversion script
2022-06-11 13:01:18 +02:00
Taniguti
547f483b74
Merge branch 'master' into haplocheck
2022-06-10 20:39:33 -03:00
Jasmin F
7027719c67
Merge branch 'master' into r-ampir
2022-06-10 14:57:24 +02:00
James A. Fellows Yates
01d4a1fa3a
Apply suggestions from code review
2022-06-10 14:46:58 +02:00
jasmezz
088b5b14f6
Merge branch 'r-ampir' of github.com:jasmezz/modules into r-ampir
2022-06-10 12:54:47 +02:00
jasmezz
39388abc04
Add file name collision check + TSV output
2022-06-10 12:54:39 +02:00
Gisela Gabernet
5a16cf7bae
Merge branch 'master' into cellranger-7.0.0
2022-06-10 11:19:57 +02:00
Alexander Peltzer
62c4b59d10
Update main.nf
2022-06-10 11:05:59 +02:00
Thiseas C. Lamnidis
9948e9fe21
Merge branch 'master' into sexdeterrmine
2022-06-10 11:03:18 +02:00
Thiseas C. Lamnidis
fe855a1c23
Apply suggestions from code review
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-10 11:03:01 +02:00
Alexander Peltzer
cfcd93f3e7
Update Dockerfile
2022-06-10 10:56:13 +02:00
Alexander Peltzer
61d87bb2bc
Update main.nf
2022-06-10 10:54:06 +02:00
Alexander Peltzer
e499abe572
Update main.nf
2022-06-10 10:53:48 +02:00
Alexander Peltzer
8032833e6e
Update main.nf
2022-06-10 10:53:09 +02:00
Alexander Peltzer
e36b79201d
Update Dockerfile
2022-06-10 10:52:13 +02:00
James A. Fellows Yates
c9db677a45
Merge branch 'master' into r-ampir
2022-06-09 19:28:37 +02:00
jasmezz
ecf1d146ab
Add full user options for AMPir
2022-06-09 16:59:00 +02:00
Maxime U. Garcia
878a5a8093
Merge branch 'master' into update_spark
2022-06-09 15:49:31 +02:00
jasmezz
ba53e09b64
Implement suggestions from code review
2022-06-09 15:37:35 +02:00
Rike
6a4732ef3b
similar issues arise with bqsrspark, also use broadinstitute container
2022-06-09 15:29:00 +02:00
Rike
8e8f4c9c51
remove singulairty container
2022-06-09 15:16:11 +02:00
nvnieuwk
873215c8ae
Update modules/gatk4/reblockgvcf/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-09 15:11:18 +02:00
Rike
89a6a03e38
fix container tag
2022-06-09 15:09:19 +02:00
Nicolas Vannieuwkerke
81fff7384d
small fix and typo
2022-06-09 15:08:02 +02:00
Rike
b9e397ff15
use broadinstitute container
2022-06-09 15:06:46 +02:00
nvnieuwk
bf73b6d376
Merge branch 'master' into new-module-gatk4/reblockgvcf
2022-06-09 14:57:20 +02:00
