millironx/nf-core_modules
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2772 commits 30 branches 0 tags 142 MiB
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Author SHA1 Message Date
SusiJo
0708f343de
Merge branch 'master' into cnvkit_bam 2022-05-24 07:49:51 +02:00
SusiJo
361b3a458b
Merge pull request #1686 from SusiJo/cnvkit/antitarget 
Added module cnvkit/antitarget
 2022-05-24 07:48:55 +02:00
SusiJo
1451d62be4 rm md5sums for empty files 2022-05-24 07:38:53 +02:00
SusiJo
63c038ad68
Merge branch 'nf-core:master' into cnvkit_bam 2022-05-24 07:37:24 +02:00
SusiJo
b3e2f70651
Merge branch 'master' into cnvkit/antitarget 2022-05-24 07:36:07 +02:00
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
SusiJo
58c5ec2f4e
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:53:28 +02:00
SusiJo
86b5951c14
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:48:30 +02:00
SusiJo
24905e26e2
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:48:13 +02:00
SusiJo
ddb964a4bf
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:48:04 +02:00
SusiJo
5d5eacee63
Merge branch 'nf-core:master' into cnvkit/antitarget 2022-05-23 16:52:33 +02:00
SusiJo
4f9d672e55 added new module cnvkit/antitarget 2022-05-23 16:52:06 +02:00
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
SusiJo
fd31f64266
Merge branch 'master' into cnvkit_bam 2022-05-23 11:31:56 +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
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