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2748 commits 30 branches 0 tags 142 MiB
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Author SHA1 Message Date
Matthias De Smet
91f9a0711d
Merge pull request #1683 from matthdsm/update/picard 
picard: make reference sequence optional
 2022-05-23 20:06:11 +02:00
Sateesh Peri
da0ead705e
Merge branch 'master' into update/picard 2022-05-23 13:38:18 -04:00
FriederikeHanssen
51bd58809d
Merge pull request #1676 from FriederikeHanssen/gatk_filter 
Gatk filtervarianttranches
 2022-05-23 15:54:57 +02:00
FriederikeHanssen
754afa9ff3
Merge branch 'master' into gatk_filter 2022-05-23 15:37:44 +02:00
Rike
e34dcdd8bc add brackets to contains 2022-05-23 13:19:42 +02:00
Rike
dc6ad1bff6 add brackets to contains 2022-05-23 13:07:08 +02:00
Rike
093e3aafdd contains 2022-05-23 13:04:49 +02:00
Rike
a8de9fd085 test path update 2022-05-23 12:53:36 +02:00
Rike
3af61cfbbc fix input cardinality for index 2022-05-23 12:26:12 +02:00
Rike
175ea9b7f9 fix version 2022-05-23 12:15:33 +02:00
Rike
a8dac59c50 md5sum not consistent 2022-05-23 12:10:50 +02:00
Rike
2f36a44f61 nf-core create-test-yml 2022-05-23 12:00:31 +02:00
Rike
cd60b4c6eb add in testdata paths 2022-05-22 13:35:35 +02:00
Rike
5d72500d60 remove variables used for test data generation, add tbi 2022-05-22 13:34:56 +02:00
Rike
520dd06ca3 add new testdata 2022-05-22 13:25:39 +02:00
Matthias De Smet
e13fbf423e fix tests (again) 2022-05-22 06:54:09 +02:00
Matthias De Smet
cbceee9621 fix tests 2022-05-22 06:51:27 +02:00
Matthias De Smet
3a2de0cf6f update test for wgsmetrics 2022-05-22 06:49:31 +02:00
Matthias De Smet
c390385cf5 revert wgsmetrics' 2022-05-22 06:44:17 +02:00
Matthias De Smet
4da143ce62 add tests 2022-05-22 06:44:17 +02:00
Matthias De Smet
d6a0238cd1
Merge branch 'master' into update/picard 2022-05-21 08:34:33 +02:00
Matthias De Smet
a5a6973fcf picard: make reference sequence optional 2022-05-21 08:33:49 +02:00
Mahesh Binzer-Panchal
7a83ca3070
Merge pull request #1682 from mahesh-panchal/mash_screen 
Add mash screen
 2022-05-20 16:47:36 +02:00
Mahesh Binzer-Panchal
2926ec0abb Add mash screen 2022-05-20 13:23:11 +00:00
Rike
bb3e64647b Merge remote-tracking branch 'origin/master' into gatk_filter 2022-05-18 15:52:47 +02:00
FriederikeHanssen
c8ccfe3710
Merge pull request #1675 from FriederikeHanssen/gatk_cnnscore 
Gatk cnnscore
 2022-05-18 15:44:52 +02:00
FriederikeHanssen
44e9cf56fa
Merge branch 'master' into gatk_cnnscore 2022-05-18 15:32:36 +02:00
Rike
11d514cd30 Merge remote-tracking branch 'origin/gatk_cnnscore' into gatk_cnnscore 2022-05-18 14:33:15 +02:00
Rike
e8221cf98e Merge remote-tracking branch 'origin' into gatk_cnnscore 2022-05-18 14:27:25 +02:00
Rike
10840a0562 Conda not suported 2022-05-18 14:26:21 +02:00
James A. Fellows Yates
9f8d6cbdd5
Merge pull request #1616 from jianhong/motus_profile 
Motus profile
 2022-05-18 12:26:31 +01:00
James A. Fellows Yates
965fabdd54
Merge branch 'master' into motus_profile 2022-05-18 11:25:48 +01:00
Rike
5ae757121f Add indices and meta 2022-05-17 23:38:26 +02:00
FriederikeHanssen
fdf1bec20b
Merge branch 'master' into gatk_cnnscore 2022-05-17 23:07:09 +02:00
Rike
05837a011d Add comment 2022-05-17 23:06:52 +02:00
Rike
15fba1dd7c add filter variant tranches 2022-05-17 23:01:24 +02:00
Rike
afa0f2a995 update test 2022-05-17 22:53:41 +02:00
Rike
265fd882ca update test 2022-05-17 19:44:48 +02:00
Rike
5f63904a50 update test 2022-05-17 19:37:18 +02:00
Rike
05611cf27c update pytest 2022-05-17 19:11:05 +02:00
Rike
e0fcbb428d Add CNNScoreVariants 2022-05-17 19:09:46 +02:00
Matthias De Smet
856a8712f8
Merge pull request #1667 from matthdsm/biobambam/bammerge 2022-05-17 17:09:06 +02:00
Jose Espinosa-Carrasco
3614c19206
Merge branch 'master' into biobambam/bammerge 2022-05-17 15:07:37 +02:00
Jose Espinosa-Carrasco
fbf20c1e36
Merge pull request #1673 from nvnieuwk/new-module-bedtools/split 
new module: bedtools split
 2022-05-17 14:45:07 +02:00
Nicolas Vannieuwkerke
6342f5b099 added bedtools split 2022-05-17 14:24:32 +02:00
Matthias De Smet
f48790a728
replace regex with fixed extensions 2022-05-17 09:54:06 +02:00
Matthias De Smet
94733a85c0
Update modules/biobambam/bammerge/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-05-17 09:46:19 +02:00
Matthias De Smet
c5627e0274 fix config 2022-05-17 09:09:19 +02:00
Matthias De Smet
743e95c61b fix config 2022-05-17 09:01:02 +02:00
Matthias De Smet
d3ddc2221a
Merge branch 'master' into biobambam/bammerge 2022-05-17 08:26:28 +02:00