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Author SHA1 Message Date
FriederikeHanssen
754afa9ff3
Merge branch 'master' into gatk_filter 2022-05-23 15:37:44 +02:00
Thiseas Christos Lamnidis
070dee0f5b Use newly added test bam 2022-05-23 15:22:22 +02:00
jtangrot
853b76d16a Add options for output file type 2022-05-23 14:02:10 +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
Ramprasad Neethiraj
9fb327fec7 Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-05-23 13:06:00 +02:00
Rike
093e3aafdd contains 2022-05-23 13:04:49 +02:00
Ramprasad Neethiraj
06a3bff201 fix lint error 2022-05-23 12:59:48 +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
SusiJo
fd31f64266
Merge branch 'master' into cnvkit_bam 2022-05-23 11:31:56 +02:00
jtangrot
8d5680a6b7 Add vserach usearch_global 2022-05-23 10:01:55 +02:00
Mahesh Binzer-Panchal
e06fb752c3
Merge branch 'master' into kat_hist 2022-05-23 08:52:13 +02:00
Mahesh Binzer-Panchal
d7c1fe1477
Update tests/modules/kat/hist/test.yml 
Co-authored-by: Sateesh Peri <105730406+sateeshblue@users.noreply.github.com>
 2022-05-23 08:51:49 +02:00
Mahesh Binzer-Panchal
b40b147004
Update tests/modules/kat/hist/test.yml 
Co-authored-by: Sateesh Peri <105730406+sateeshblue@users.noreply.github.com>
 2022-05-23 08:51:29 +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
Ramprasad Neethiraj
995bf88327 add stub 2022-05-20 17:10:09 +02:00
Ramprasad Neethiraj
635edc0022 fix typo 2022-05-20 17:07:42 +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
Ramprasad Neethiraj
2542c9d176 add tests 2022-05-20 16:46:19 +02:00
Mahesh Binzer-Panchal
2926ec0abb Add mash screen 2022-05-20 13:23:11 +00:00
Ramprasad Neethiraj
c70b169f61 create modules 2022-05-20 13:34:54 +02:00
SusiJo
9096be5464 improve readability 2022-05-20 13:29:49 +02:00
SusiJo
bdf222649d remove unnecessary if statement 2022-05-20 13:25:57 +02:00
SusiJo
153c900d0e
refine comment 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-20 13:08:38 +02:00
SusiJo
2e5aa0dbb4
refine comment 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-20 13:08:26 +02:00
SusiJo
3b3921cfa3
refine comment 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-20 13:07:57 +02:00
SusiJo
00077c36c8 removed unnecessary fasta for tumor_only_bam 2022-05-20 13:06:16 +02:00
SusiJo
f392c4bed5 removed params section & added description fasta 2022-05-20 13:05:43 +02:00
SusiJo
129270d7bc adjusted conda env & singularity container 2022-05-20 10:37:46 +02:00
SusiJo
dd2f48810a
Merge branch 'nf-core:master' into cnvkit_bam 2022-05-20 09:14:21 +02:00
SusiJo
3d57caa683 added test & corrected cram input 2022-05-20 09:13:27 +02:00
SusiJo
5a1297cc7d added optional pdf/png outputs 2022-05-20 09:12:47 +02:00
SusiJo
064712c4ea added cram_bam conversion & tumor_only check 2022-05-20 09:11:45 +02:00
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