SusiJo
|
153c900d0e
|
refine comment
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-20 13:08:38 +02:00 |
|
SusiJo
|
2e5aa0dbb4
|
refine comment
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-20 13:08:26 +02:00 |
|
SusiJo
|
3b3921cfa3
|
refine comment
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-20 13:07:57 +02:00 |
|
SusiJo
|
f392c4bed5
|
removed params section & added description fasta
|
2022-05-20 13:05:43 +02:00 |
|
SusiJo
|
129270d7bc
|
adjusted conda env & singularity container
|
2022-05-20 10:37:46 +02:00 |
|
SusiJo
|
dd2f48810a
|
Merge branch 'nf-core:master' into cnvkit_bam
|
2022-05-20 09:14:21 +02:00 |
|
SusiJo
|
5a1297cc7d
|
added optional pdf/png outputs
|
2022-05-20 09:12:47 +02:00 |
|
SusiJo
|
064712c4ea
|
added cram_bam conversion & tumor_only check
|
2022-05-20 09:11:45 +02:00 |
|
Rike
|
bb3e64647b
|
Merge remote-tracking branch 'origin/master' into gatk_filter
|
2022-05-18 15:52:47 +02:00 |
|
FriederikeHanssen
|
44e9cf56fa
|
Merge branch 'master' into gatk_cnnscore
|
2022-05-18 15:32:36 +02:00 |
|
Rike
|
e8221cf98e
|
Merge remote-tracking branch 'origin' into gatk_cnnscore
|
2022-05-18 14:27:25 +02:00 |
|
Rike
|
10840a0562
|
Conda not suported
|
2022-05-18 14:26:21 +02:00 |
|
James A. Fellows Yates
|
965fabdd54
|
Merge branch 'master' into motus_profile
|
2022-05-18 11:25:48 +01:00 |
|
Rike
|
5ae757121f
|
Add indices and meta
|
2022-05-17 23:38:26 +02:00 |
|
Rike
|
05837a011d
|
Add comment
|
2022-05-17 23:06:52 +02:00 |
|
Rike
|
15fba1dd7c
|
add filter variant tranches
|
2022-05-17 23:01:24 +02:00 |
|
Rike
|
e0fcbb428d
|
Add CNNScoreVariants
|
2022-05-17 19:09:46 +02:00 |
|
Jose Espinosa-Carrasco
|
3614c19206
|
Merge branch 'master' into biobambam/bammerge
|
2022-05-17 15:07:37 +02:00 |
|
Nicolas Vannieuwkerke
|
6342f5b099
|
added bedtools split
|
2022-05-17 14:24:32 +02:00 |
|
Matthias De Smet
|
f48790a728
|
replace regex with fixed extensions
|
2022-05-17 09:54:06 +02:00 |
|
Matthias De Smet
|
94733a85c0
|
Update modules/biobambam/bammerge/main.nf
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
|
2022-05-17 09:46:19 +02:00 |
|
Matthias De Smet
|
d3ddc2221a
|
Merge branch 'master' into biobambam/bammerge
|
2022-05-17 08:26:28 +02:00 |
|
Matthias De Smet
|
6be91ce82d
|
fix optional output detection
|
2022-05-17 08:20:47 +02:00 |
|
Subazini TK
|
79c2c529fc
|
Merge branch 'master' into hmtnote
|
2022-05-17 08:05:47 +02:00 |
|
JIANHONG OU
|
671bacb6df
|
Merge branch 'master' into motus_profile
|
2022-05-16 17:34:49 -04:00 |
|
Matthias De Smet
|
d0db186e84
|
Merge branch 'master' into biobambam/bammerge
|
2022-05-16 20:52:48 +02:00 |
|
Matthias De Smet
|
a79b9adeee
|
address review comments
|
2022-05-16 20:51:39 +02:00 |
|
Subazini TK
|
00204fa82b
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
a0b46d3f03
|
Update meta.yml
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
eaf81f6835
|
Update meta.yml
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
1c42c97504
|
Update meta.yml
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
8b4c5742c9
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
2a15bc2ac0
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
|
78dc1af1e6
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
sysbiocoder
|
26f026683b
|
hmtnote
|
2022-05-16 15:20:15 +00:00 |
|
sysbiocoder
|
31fc8b560f
|
hmtnote
|
2022-05-16 15:20:15 +00:00 |
|
Veit Schwämmle
|
85345e5f61
|
Merge branch 'master' into maxquant
|
2022-05-16 16:06:32 +02:00 |
|
Praveen Raj S
|
df2620cfc7
|
Merge branch 'master' into process_lable_markdup
|
2022-05-16 15:53:26 +02:00 |
|
Matthias De Smet
|
98f204fd1f
|
Update modules/biobambam/bammerge/main.nf
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
|
2022-05-16 15:13:54 +02:00 |
|
Matthias De Smet
|
cdbe648400
|
align
|
2022-05-16 14:44:32 +02:00 |
|
Matthias De Smet
|
2cca156fed
|
linting
|
2022-05-16 14:42:34 +02:00 |
|
Matthias De Smet
|
af69ea749d
|
add module: biobambam/bammerge
|
2022-05-16 14:39:58 +02:00 |
|
veitveit
|
12815af53e
|
ran prettier
|
2022-05-16 14:30:40 +02:00 |
|
Veit Schwämmle
|
74a1c1400e
|
Merge branch 'master' into maxquant
|
2022-05-16 13:26:35 +02:00 |
|
Jasmin F
|
982c9183fa
|
Merge branch 'master' into antismashlite
|
2022-05-16 11:42:44 +02:00 |
|
Jasmin F
|
adcfae6cd4
|
Merge branch 'master' into antismashlite
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2022-05-16 10:38:01 +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 |
|
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 |
|
Nicolas Vannieuwkerke
|
6427eeeca0
|
added tmp-dir + alignment correction
|
2022-05-13 14:35:22 +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
|
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 |
|
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
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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 |
|
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
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f6262b4a10
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fixed some issues
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2022-05-09 15:47:07 +02:00 |
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Rike
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24d5e7feed
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Code review suggestions
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2022-05-09 15:42:55 +02:00 |
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Mahesh Binzer-Panchal
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8d86988632
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Merge branch 'master' into meryl/histogram
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2022-05-09 15:39:32 +02:00 |
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Rike
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ef5f145342
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Generalize Bam2Cram do either conversion
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2022-05-09 15:22:54 +02:00 |
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Mahesh Binzer-Panchal
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57fee2b3d6
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Add description pattern
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2022-05-09 12:56:22 +00:00 |
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Annick Renevey
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bf91f9dd9b
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update arriba module
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2022-05-09 14:55:59 +02:00 |
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Mahesh Binzer-Panchal
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6621768550
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Update pytest outputs
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2022-05-09 12:54:31 +00:00 |
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Mahesh Binzer-Panchal
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ce97c87b5d
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Merge branch 'master' into meryl_unionsum
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2022-05-09 13:51:55 +02:00 |
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Mahesh Binzer-Panchal
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7a5d5f5766
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Merge branch 'master' into kat_hist
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2022-05-09 13:18:18 +02:00 |
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Mahesh Binzer-Panchal
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a43bc940d6
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Add suggestions from code review
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2022-05-09 11:15:14 +00:00 |
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Mahesh Binzer-Panchal
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129f57ccd9
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Add meryl histogram
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2022-05-09 08:50:28 +00:00 |
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Mahesh Binzer-Panchal
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ad4f8389cb
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Add meryl unionsum
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2022-05-09 08:33:21 +00:00 |
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Mahesh Binzer-Panchal
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32b0fdc9d9
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Merge branch 'master' into meryl_count
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2022-05-09 10:05:28 +02:00 |
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Mahesh Binzer-Panchal
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4591ea2205
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atomize
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2022-05-09 07:58:58 +00:00 |
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