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2897 commits 30 branches 0 tags 142 MiB
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1064 commits

Author SHA1 Message Date
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
Mahesh Binzer-Panchal
308ab8801d
Merge branch 'master' into kat_hist 2022-05-12 16:52:05 +02:00
Rike
f40cfefc08 leftover fixes from refactoring 2022-05-12 16:47:17 +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
JIANHONG OU
6b960f0e75 fix the typo in motus_profile. 2022-05-12 09:20:32 -04:00
James A. Fellows Yates
3c02e6056c
Merge branch 'master' into antismashlite 2022-05-12 14:53:52 +02:00
Chris Cheshire
90c67794bf Added extra tests but error with collection 2022-05-12 10:01:33 +01:00
jasmezz
bd4b70439b Streamlined some output channels, formatted tests main.nf 2022-05-12 10:56:48 +02:00
JIANHONG OU
a2dbef3de3 remove the wrong quotes for motus_profile. 2022-05-11 17:49:12 -04:00
JIANHONG OU
aca4b48842 Merge branch 'motus_profile' of github.com:jianhong/modules into motus_profile 2022-05-11 14:23:25 -04:00
JIANHONG OU
ae81311a78 fix the typo when using getExtension for motus_profile. 2022-05-11 14:23:09 -04:00
Matthias De Smet
dcf9c07fc9
Merge branch 'master' into update/bowtie2-align 2022-05-11 19:08:23 +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
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
Mahesh Binzer-Panchal
0199d0efd2
Merge branch 'master' into kat_hist 2022-05-11 16:56:29 +02:00
Matthias De Smet
c8d3de2ad9
restore samtools cmd to defaults 2022-05-11 16:17:30 +02:00
Jasmin F
853e3ec087
Remove commented code 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-05-11 15:56:10 +02:00
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
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
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
Moritz E. Beber
0cdf7767a7 refactor: require NCBI user settings always 2022-05-11 13:02:52 +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
7be7f404d5
Merge branch 'master' into refactor-prefetch 2022-05-11 11:28:02 +01:00
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
Mahesh Binzer-Panchal
cd32c7f744
Merge branch 'master' into kat_hist 2022-05-10 17:03:00 +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
Nicolas Vannieuwkerke
fa7c947c35 Adjusted meta 2022-05-10 13:33:37 +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