Nicolas Vannieuwkerke
|
8a17b6dd0e
|
added gatk4/splitintervals
|
2022-05-13 13:46:34 +02:00 |
|
Chris Cheshire
|
9f6a1ae4a4
|
Merge branch 'master' into bowtie2-test-fix
|
2022-05-13 12:05:48 +01:00 |
|
Mahesh Binzer-Panchal
|
00826dc2e9
|
Merge branch 'master' into genomescope2
|
2022-05-13 11:28:47 +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
|
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 |
|
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
|
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 |
|
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 |
|
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
|
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
|
e5d091ad4b
|
Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval
|
2022-05-10 09:35:44 +02:00 |
|
Nicolas Vannieuwkerke
|
c69d5cc23e
|
Added evaluation-regions and adjusted the output to now contain all output (and not only the summary)
|
2022-05-10 09:35:42 +02:00 |
|
nvnieuwk
|
95103fbd79
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-10 09:06:34 +02:00 |
|
Praveen Raj S
|
459a2d1759
|
Merge branch 'master' into master
|
2022-05-09 22:16:59 +02:00 |
|
Mahesh Binzer-Panchal
|
f65d896f57
|
create genomescope2 module
|
2022-05-09 15:09:15 +00:00 |
|
Mahesh Binzer-Panchal
|
705ad7c3a1
|
Merge branch 'master' into meryl_unionsum
|
2022-05-09 16:20:01 +02:00 |
|
nvnieuwk
|
aceb5220cf
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-09 16:18:00 +02:00 |
|
Mahesh Binzer-Panchal
|
83a266ea70
|
Merge branch 'master' into meryl_unionsum
|
2022-05-09 16:16:08 +02:00 |
|
FriederikeHanssen
|
adc4ff868c
|
Merge branch 'master' into samtools_convert
|
2022-05-09 16:15:24 +02:00 |
|
Rike
|
da79396f06
|
rename aligned to alignment
|
2022-05-09 16:07:49 +02:00 |
|
Rike
|
5bd456e5e8
|
rename file_type to output extension
|
2022-05-09 16:06:22 +02:00 |
|
Rike
|
1de1c2253e
|
Combine output after code review
|
2022-05-09 16:04:58 +02:00 |
|
Nicolas Vannieuwkerke
|
bd7e1414a4
|
Fixed meta.yml
|
2022-05-09 15:55:48 +02:00 |
|
nvnieuwk
|
4b8bd9ebf9
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-09 15:51:31 +02:00 |
|
Nicolas Vannieuwkerke
|
1b63d03f8e
|
adjusted the bed variable name
|
2022-05-09 15:51:19 +02:00 |
|
Nicolas Vannieuwkerke
|
f6262b4a10
|
fixed some issues
|
2022-05-09 15:47:07 +02:00 |
|
Rike
|
24d5e7feed
|
Code review suggestions
|
2022-05-09 15:42:55 +02:00 |
|
Mahesh Binzer-Panchal
|
8d86988632
|
Merge branch 'master' into meryl/histogram
|
2022-05-09 15:39:32 +02:00 |
|
Rike
|
ef5f145342
|
Generalize Bam2Cram do either conversion
|
2022-05-09 15:22:54 +02:00 |
|
Mahesh Binzer-Panchal
|
57fee2b3d6
|
Add description pattern
|
2022-05-09 12:56:22 +00:00 |
|
Annick Renevey
|
bf91f9dd9b
|
update arriba module
|
2022-05-09 14:55:59 +02:00 |
|
Mahesh Binzer-Panchal
|
6621768550
|
Update pytest outputs
|
2022-05-09 12:54:31 +00:00 |
|
Mahesh Binzer-Panchal
|
ce97c87b5d
|
Merge branch 'master' into meryl_unionsum
|
2022-05-09 13:51:55 +02:00 |
|
Mahesh Binzer-Panchal
|
a43bc940d6
|
Add suggestions from code review
|
2022-05-09 11:15:14 +00:00 |
|
Mahesh Binzer-Panchal
|
129f57ccd9
|
Add meryl histogram
|
2022-05-09 08:50:28 +00:00 |
|
Mahesh Binzer-Panchal
|
ad4f8389cb
|
Add meryl unionsum
|
2022-05-09 08:33:21 +00:00 |
|
Mahesh Binzer-Panchal
|
32b0fdc9d9
|
Merge branch 'master' into meryl_count
|
2022-05-09 10:05:28 +02:00 |
|
Mahesh Binzer-Panchal
|
4591ea2205
|
atomize
|
2022-05-09 07:58:58 +00:00 |
|
Matthias De Smet
|
2b91985aa0
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-09 09:43:48 +02:00 |
|
Nicolas Vannieuwkerke
|
d18af7358a
|
Moved untarring the genome sdf folder to the test itself
|
2022-05-09 09:20:42 +02:00 |
|
James A. Fellows Yates
|
8a83ad0518
|
Merge branch 'master' into motus_profile
|
2022-05-09 08:16:16 +02:00 |
|
nvnieuwk
|
6fd9246aef
|
Update modules/rtgtools/vcfeval/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
|
2022-05-09 08:07:33 +02:00 |
|
JIANHONG OU
|
b2542ee079
|
remove the mgc in metadata for motus_profile.
|
2022-05-08 06:21:26 -04:00 |
|
Harshil Patel
|
2676f8eef4
|
Merge branch 'master' into fix-prefetch
|
2022-05-06 19:33:44 +01:00 |
|
Matthias De Smet
|
0752b82c9f
|
Merge branch 'master' into update/snapaligner
|
2022-05-06 18:57:37 +02:00 |
|
Moritz E. Beber
|
ea41c753c0
|
fix: remove retry label
Call gets retried by bash script
|
2022-05-06 17:28:56 +02:00 |
|
Moritz E. Beber
|
dd1c66783a
|
refactor: use a template to add retrying
|
2022-05-06 17:26:41 +02:00 |
|
Moritz E. Beber
|
ed09978222
|
chore: update build number
|
2022-05-06 17:26:41 +02:00 |
|
Mahesh Binzer-Panchal
|
67481c6d54
|
Start Meryl count
|
2022-05-06 15:04:04 +00:00 |
|
Nicolas Vannieuwkerke
|
eb8688d2b8
|
Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval
|
2022-05-06 16:21:35 +02:00 |
|
Nicolas Vannieuwkerke
|
e271410017
|
Removed some whitespaces
|
2022-05-06 16:21:32 +02:00 |
|