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Author SHA1 Message Date
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
fd579ebbb3
Merge branch 'master' into kat_hist 2022-05-11 12:43:11 +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
Harshil Patel
7be7f404d5
Merge branch 'master' into refactor-prefetch 2022-05-11 11:28:02 +01:00
jasmezz
2b746abfbe Fix Prettier linting issue 2022-05-11 12:09:52 +02:00
jasmezz
5d76f1c7ff Add fasta/gff input option 2022-05-11 12:06:02 +02:00
Jasmin F
9cce4a00b2
Merge branch 'nf-core:master' into antismashlite 2022-05-11 12:03:30 +02:00
Mahesh Binzer-Panchal
0774704038
Merge branch 'master' into genomescope2 2022-05-11 11:38:36 +02:00
Robert A. Petit III
ef2996e4a5 match names in meta and main 2022-05-10 21:47:57 +00:00
Robert A. Petit III
56e94f625e remove empty file md5 2022-05-10 21:47:11 +00:00
Robert A. Petit III
f15848d477 fix typo 2022-05-10 21:44:40 +00:00
Robert A. Petit III
44e13ae439 add module for snippy 2022-05-10 21:31:43 +00:00
Mahesh Binzer-Panchal
7a16ece747 Change md5sum to contains 2022-05-10 15:13:25 +00:00
Mahesh Binzer-Panchal
cd32c7f744
Merge branch 'master' into kat_hist 2022-05-10 17:03:00 +02:00
Mahesh Binzer-Panchal
9b4923dcd5 Change test files 2022-05-10 15:02:37 +00:00
Praveen Raj S
ae55653c3c
Merge pull request #1638 from rannick/master 
Update arriba
 2022-05-10 14:39:29 +02:00
Mahesh Binzer-Panchal
b875cfb744
Merge branch 'master' into kat_hist 2022-05-10 14:36:18 +02:00
Praveen Raj S
237971cd15
Merge branch 'master' into master 2022-05-10 14:35:41 +02:00
nvnieuwk
914e56163a
Merge pull request #1624 from nvnieuwk/new-module-rtg/vcfeval 
New module rtg/vcfeval
 2022-05-10 13:41:20 +02:00
Nicolas Vannieuwkerke
c9cd7be8df Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval 2022-05-10 13:33:40 +02:00
Nicolas Vannieuwkerke
fa7c947c35 Adjusted meta 2022-05-10 13:33:37 +02:00
nvnieuwk
d3927aae99
Update modules/rtgtools/vcfeval/main.nf 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-05-10 13:26:14 +02:00
nvnieuwk
7fc4cc5a38
Update modules/rtgtools/vcfeval/main.nf 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-05-10 13:23:22 +02:00
Nicolas Vannieuwkerke
b7134855e4 Small update on the output channels 2022-05-10 12:34:52 +02:00
Moritz E. Beber
1b228835e9 refactor: require settings input always 2022-05-10 12:29:42 +02:00
Nicolas Vannieuwkerke
c18391aa49 Updated meta.yml 2022-05-10 12:26:13 +02:00
nvnieuwk
2eb77bd64e
Update modules/rtgtools/vcfeval/main.nf 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-05-10 12:22:56 +02:00
nvnieuwk
29f2d3c284
Update modules/rtgtools/vcfeval/main.nf 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-05-10 12:22:49 +02:00
Nicolas Vannieuwkerke
ef4857ec54 Updated meta.yml 2022-05-10 12:20:01 +02:00
Moritz E. Beber
a303904eb0 chore: add settings file to test data config 2022-05-10 12:19:25 +02:00
Moritz E. Beber
09bfe3c618 Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-10 12:16:57 +02:00
Moritz E. Beber
b1e134fdd7 docs: describe new file input 2022-05-10 12:16:57 +02:00
Moritz E. Beber
145e2f80e9 tests: run prefetch with and without given settings 2022-05-10 12:16:57 +02:00
Moritz E. Beber
f6936e5270 refactor: accept settings as input 2022-05-10 12:16:57 +02:00
Moritz E. Beber
46a9aabfa3 chore: improve license description 2022-05-10 12:16:57 +02:00
Nicolas Vannieuwkerke
f3d5584ab0 Linting 2022-05-10 12:08:23 +02:00
Nicolas Vannieuwkerke
5db26f9f35 Linting 2022-05-10 12:07:11 +02:00
Nicolas Vannieuwkerke
3a064b0a99 Split the output to different channels 2022-05-10 12:05:42 +02:00
Nicolas Vannieuwkerke
6008619603 test issue fix? 2022-05-10 10:20:54 +02:00