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Author SHA1 Message Date
FriederikeHanssen
0b0556b57f
Merge pull request #1649 from FriederikeHanssen/gatk_426 
update gatk version to 4.2.6.1
 2022-05-16 11:24:14 +02:00
Rike
eb841d4ea0 revert markduplciatespark changes 2022-05-16 10:33:01 +02:00
Rike
ba14355891 revert markduplciatespark changes 2022-05-16 09:54:40 +02:00
FriederikeHanssen
8b4d021189
Merge branch 'master' into gatk_426 2022-05-16 09:50:13 +02:00
Jose Espinosa-Carrasco
759223d22d
Merge pull request #1660 from matthdsm/update/bowtie2 
Bowtie2: add sort option
 2022-05-13 20:23:04 +02:00
Matthias De Smet
5a2e303522 add PE sorted test 2022-05-13 19:16:50 +02:00
Matthias De Smet
04f82d4d34 fix test name 2022-05-13 15:32:14 +02:00
Matthias De Smet
cbc47767f7 add sort option to bowtie2 2022-05-13 15:26:41 +02:00
nvnieuwk
919275103a
Merge pull request #1655 from nvnieuwk/new-module-gatk4/splitintervals 
new module: gatk4/splitintervals
 2022-05-13 14:43:15 +02:00
Nicolas Vannieuwkerke
6427eeeca0 added tmp-dir + alignment correction 2022-05-13 14:35:22 +02:00
Nicolas Vannieuwkerke
a72f06dfe8 removed versions checksum 2022-05-13 14:27:59 +02:00
Nicolas Vannieuwkerke
1c2a991429 fixed memory warning 2022-05-13 14:25:53 +02:00
Nicolas Vannieuwkerke
d1f824ae66 updated meta.yml 2022-05-13 14:21:48 +02:00
Nicolas Vannieuwkerke
4f6264f7c3 Merge branch 'new-module-gatk4/splitintervals' of github.com:nvnieuwk/modules into new-module-gatk4/splitintervals 2022-05-13 13:48:35 +02:00
Nicolas Vannieuwkerke
9d53577282 linting 2022-05-13 13:48:33 +02:00
nvnieuwk
1d4862ba60
Merge branch 'master' into new-module-gatk4/splitintervals 2022-05-13 13:47:20 +02:00
Nicolas Vannieuwkerke
8a17b6dd0e added gatk4/splitintervals 2022-05-13 13:46:34 +02:00
Chris Cheshire
af017b32a5
Merge pull request #1653 from luslab/bowtie2-test-fix 
Bowtie2 test fixes
 2022-05-13 12:32:28 +01:00
Chris Cheshire
ea55129ba3 Removed version file checksums 2022-05-13 12:20:41 +01:00
Chris Cheshire
9f6a1ae4a4
Merge branch 'master' into bowtie2-test-fix 2022-05-13 12:05:48 +01:00
Chris Cheshire
d816f2bc5d Reactivated all tests 2022-05-13 12:01:16 +01:00
Mahesh Binzer-Panchal
4acbf9d356
Merge pull request #1641 from mahesh-panchal/genomescope2 
Genomescope2 module
 2022-05-13 11:37:49 +02:00
Mahesh Binzer-Panchal
00826dc2e9
Merge branch 'master' into genomescope2 2022-05-13 11:28:47 +02:00
Mahesh Binzer-Panchal
5df0bcf1be
Update tests/modules/genomescope2/test.yml 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-13 11:27:42 +02:00
Matthias De Smet
fc987d5fcd
Merge pull request #1650 from nvnieuwk/update-module-rtgtools/vcfeval 
Added memory allocation to VCFeval
 2022-05-13 10:55:32 +02:00
Nicolas Vannieuwkerke
6fa1c8089a Added memory allocation to VCFeval 2022-05-13 10:03:20 +02:00
FriederikeHanssen
868150e1af
Merge branch 'master' into gatk_426 2022-05-12 19:33:07 +02:00
Rike
5f7b02189a reverse again, why did tests pass before 2022-05-12 18:35:51 +02:00
Rike
e3a17b699e update version 2022-05-12 18:19:33 +02:00
Rike
99880654bf add output default bam 2022-05-12 18:06:15 +02:00
Rike
3fda3903dc revert markduplciatespark container 2022-05-12 17:40:42 +02:00
Rike
8792d102ee fix test input 2022-05-12 17:37:06 +02:00
Rike
a694267b4b fix empty index input 2022-05-12 17:01:03 +02:00
Rike
b3bd55da76 getpileupsummaries requires intervals files 2022-05-12 16:51:17 +02:00
Rike
f40cfefc08 leftover fixes from refactoring 2022-05-12 16:47:17 +02:00
Rike
15fbf21b28 double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere 2022-05-12 16:16:53 +02:00
Rike
fef5434c4c Update md5sums 2022-05-12 16:07:12 +02:00
Rike
fd7ee6799a update version also for spark containers 2022-05-12 15:55:11 +02:00
Rike
169b2b96c1 update gatk version 2022-05-12 15:45:21 +02:00
Harshil Patel
be0f022053
Merge pull request #1648 from nf-core/refactor-sra-fastq 
refactor: rename and update subworkflow
 2022-05-12 11:26:15 +01:00
Chris Cheshire
90c67794bf Added extra tests but error with collection 2022-05-12 10:01:33 +01:00
Chris Cheshire
4bb0423a1d Merge remote-tracking branch 'nf-core/master' 2022-05-12 08:57:56 +01:00
Moritz E. Beber
74b11ccc44 refactor: rename and update subworkflow 2022-05-11 19:24:16 +02:00
Matthias De Smet
1dccf12077
Merge pull request #1645 from matthdsm/update/bowtie2-align 
bowtie2: remove code duplication
 2022-05-11 19:12:23 +02:00
Matthias De Smet
dcf9c07fc9
Merge branch 'master' into update/bowtie2-align 2022-05-11 19:08:23 +02:00
Harshil Patel
4aaff98c49
Merge pull request #1630 from nf-core/add-ncbi-settings 
feat: add module that verifies NCBI settings
 2022-05-11 17:51:24 +01:00
Moritz E. Beber
98d8a741ec tests: add missing paths to config 2022-05-11 18:17:27 +02:00
Moritz E. Beber
888620063b tests: delete settings for conda 2022-05-11 17:44:49 +02:00
Moritz E. Beber
b2dbaa9930 refactor: rename module 2022-05-11 17:33:45 +02:00
Moritz E. Beber
23091aabda refactor: move files to custom section 2022-05-11 17:33:45 +02:00