Commit graph

3235 commits

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
Jasmin F
adcfae6cd4
Merge branch 'master' into antismashlite 2022-05-16 10:38:01 +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
Taniguti
ac7fe89a78
Merge branch 'master' into haplocheck 2022-05-13 11:24:10 -03:00
Matthias De Smet
04f82d4d34 fix test name 2022-05-13 15:32:14 +02:00
JIANHONG OU
fadb83cf44
Merge branch 'master' into motus_profile 2022-05-13 09:30:20 -04:00
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
Praveen
e0dccbb5dd Changed process label to Medium for GATK4/MarkDuplicates 2022-05-13 13:55:14 +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
Taniguti
4728b2bcd2
Merge branch 'master' into haplocheck 2022-05-13 07:49:55 -03:00
Lucas Taniguti
c1ed4e21be tests: add haplocheck tests 2022-05-13 07:42:34 -03:00
Lucas Taniguti
86343cb034 feat: add haplocheck 2022-05-13 07:42:09 -03:00
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
James A. Fellows Yates
2eebab4f35
Update tests/modules/motus/profile/test.yml 2022-05-12 20:55:54 +01:00
James A. Fellows Yates
8dd711aba2
Update tests/modules/motus/profile/main.nf 2022-05-12 20:08:37 +01:00
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
Mahesh Binzer-Panchal
308ab8801d
Merge branch 'master' into kat_hist 2022-05-12 16:52:05 +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
Jasmin F
85b3c2bcf2
Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-12 15:28:19 +02:00