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Author SHA1 Message Date
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
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
Moritz E. Beber
a83dd33a7e tests: use remove settings file 2022-05-11 17:33:45 +02:00
Moritz E. Beber
e4551a9ab3 refactor: always output settings 2022-05-11 17:33:45 +02:00
Moritz E. Beber
64ff23f3c1 feat: add module that verifies NCBI settings 2022-05-11 17:33:45 +02:00
Harshil Patel
4e603393c3
Merge branch 'master' into update/bowtie2-align 2022-05-11 15:47:37 +01:00
Matthias De Smet
c8d3de2ad9
restore samtools cmd to defaults 2022-05-11 16:17:30 +02:00
Mahesh Binzer-Panchal
64dad04b9b
Merge pull request #1646 from mahesh-panchal/fix_test_config 
Fix path
 2022-05-11 15:58:55 +02:00
Mahesh Binzer-Panchal
fbe2f85e7b Fix path 2022-05-11 13:53:38 +00:00
Matthias De Smet
bcd7fe55b1
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:59:03 +02:00
Matthias De Smet
9097abf277
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:58:58 +02:00
Matthias De Smet
971a889e2a
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:57:27 +02:00
Matthias De Smet
b456d8fa0a
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:57:19 +02:00
Matthias De Smet
ff4b297827
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:57:11 +02:00
Matthias De Smet
94e8c3a882
Update tests/modules/bowtie2/align/test.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:56:03 +02:00
Matthias De Smet
9dd083fa94
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:55:55 +02:00
Matthias De Smet
0d00452eca
Update tests/modules/bowtie2/align/test.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:55:45 +02:00
Matthias De Smet
dcffd93875
Merge branch 'master' into update/bowtie2-align 2022-05-11 13:34:24 +02:00
CMGG ICT Team
3ae8cbfad7 bowtie2: remove code duplication 2022-05-11 13:32:56 +02:00
Harshil Patel
9602b989eb
Merge pull request #1632 from nf-core/refactor-fasterq-dump 
Refactor fasterq dump
 2022-05-11 12:14:22 +01:00
Moritz E. Beber
0cdf7767a7 refactor: require NCBI user settings always 2022-05-11 13:02:52 +02:00
Moritz E. Beber
eae7161a32 tests: add settings input or not and test all branches 2022-05-11 12:47:54 +02:00
Moritz E. Beber
d4f13ebfff refactor: create new settings input 2022-05-11 12:47:54 +02:00
Moritz E. Beber
5d593bdb45 docs: correct license and input description 2022-05-11 12:47:54 +02:00
Mahesh Binzer-Panchal
00fcdd0cba
Merge branch 'master' into genomescope2 2022-05-11 12:42:39 +02:00
Mahesh Binzer-Panchal
d54cf467f4 Update outputs and test data set 2022-05-11 10:42:17 +00:00
Harshil Patel
79bf60fa11
Merge pull request #1631 from nf-core/refactor-prefetch 
Refactor prefetch
 2022-05-11 11:29:02 +01:00