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Author SHA1 Message Date
Thiseas C. Lamnidis
fe855a1c23
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-10 11:03:01 +02:00
Thiseas C. Lamnidis
6d04395c3c
Merge branch 'master' into sexdeterrmine 2022-05-24 13:17:37 +02:00
Harshil Patel
300e607a61
Merge pull request #1689 from drpatelh/umitools 
Update umitools/dedup module to make --output-stats optional
 2022-05-24 09:24:03 +01:00
Harshil Patel
ec141dba08
Merge branch 'master' into umitools 2022-05-24 09:23:20 +01:00
SusiJo
0e1bbe5b4a
Merge pull request #1690 from SusiJo/cnvkit_reference 
Add cnvkit/reference module
 2022-05-24 09:08:13 +02:00
SusiJo
0f0d555f96
Merge branch 'master' into cnvkit_reference 2022-05-24 08:03:44 +02:00
SusiJo
61ebf89fb8
Merge pull request #1680 from SusiJo/cnvkit_bam 
Modified cnvkit/batch module: cram2bam conversion
 2022-05-24 08:03:26 +02:00
SusiJo
0708f343de
Merge branch 'master' into cnvkit_bam 2022-05-24 07:49:51 +02:00
SusiJo
50128b0c86
Merge branch 'master' into cnvkit_reference 2022-05-24 07:49:44 +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
SusiJo
33a72367c6
Merge branch 'nf-core:master' into cnvkit_reference 2022-05-24 07:30:29 +02:00
Harshil Patel
a3e70777ad Fix Conda tests 2022-05-23 22:39:12 +01:00
Harshil Patel
84f02a08a5 Update umitools/dedup module to make --output-stats optional 2022-05-23 22:31:09 +01:00
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
8fec7ae321 added new testdata path 2022-05-23 19:01:46 +02:00
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
bbee9e3c3b add new module cnvkit/reference 2022-05-23 18:35:50 +02:00
Thiseas Christos Lamnidis
37c6fb8fed Merge remote-tracking branch 'upstream/master' into sexdeterrmine 2022-05-23 17:30:21 +02:00
Thiseas Christos Lamnidis
96260ced83 Add test data to config 2022-05-23 17:15:57 +02:00
Thiseas Christos Lamnidis
9011fc7212 Corrected test-datasets input 2022-05-23 17:08:40 +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
Thiseas Christos Lamnidis
070dee0f5b Use newly added test bam 2022-05-23 15:22:22 +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