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1275 commits

Author SHA1 Message Date
Matthias De Smet
b5850fd471 add stub 2022-05-24 12:16:03 +02:00
Harshil Patel
393f23274d
Merge branch 'master' into cnvkit/reference 2022-05-24 11:14:50 +01:00
Harshil Patel
29a4f112be
Update main.nf 2022-05-24 11:14:32 +01:00
Matthias De Smet
01fb8851c3 mosdept: cram compatiblility 2022-05-24 11:47:58 +02:00
Harshil Patel
ec141dba08
Merge branch 'master' into umitools 2022-05-24 09:23:20 +01:00
SusiJo
5db94ea0ee changed tag of module 2022-05-24 10:17:41 +02:00
Ramprasad Neethiraj
b4982ff6e3
Merge branch 'master' into rhocall 2022-05-24 09:41:30 +02:00
SusiJo
0f0d555f96
Merge branch 'master' into cnvkit_reference 2022-05-24 08:03:44 +02:00
SusiJo
0708f343de
Merge branch 'master' into cnvkit_bam 2022-05-24 07:49:51 +02:00
SusiJo
50128b0c86
Merge branch 'master' into cnvkit_reference 2022-05-24 07:49:44 +02:00
SusiJo
63c038ad68
Merge branch 'nf-core:master' into cnvkit_bam 2022-05-24 07:37:24 +02:00
SusiJo
b3e2f70651
Merge branch 'master' into cnvkit/antitarget 2022-05-24 07:36:07 +02:00
SusiJo
33a72367c6
Merge branch 'nf-core:master' into cnvkit_reference 2022-05-24 07:30:29 +02:00
Harshil Patel
84f02a08a5 Update umitools/dedup module to make --output-stats optional 2022-05-23 22:31:09 +01:00
Sateesh Peri
da0ead705e
Merge branch 'master' into update/picard 2022-05-23 13:38:18 -04:00
SusiJo
58c5ec2f4e
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:53:28 +02:00
SusiJo
86b5951c14
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:48:30 +02:00
SusiJo
24905e26e2
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:48:13 +02:00
SusiJo
ddb964a4bf
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:48:04 +02:00
SusiJo
bbee9e3c3b add new module cnvkit/reference 2022-05-23 18:35:50 +02:00
Thiseas Christos Lamnidis
37c6fb8fed Merge remote-tracking branch 'upstream/master' into sexdeterrmine 2022-05-23 17:30:21 +02:00
SusiJo
5d5eacee63
Merge branch 'nf-core:master' into cnvkit/antitarget 2022-05-23 16:52:33 +02:00
SusiJo
4f9d672e55 added new module cnvkit/antitarget 2022-05-23 16:52:06 +02:00
FriederikeHanssen
754afa9ff3
Merge branch 'master' into gatk_filter 2022-05-23 15:37:44 +02:00
Ramprasad Neethiraj
9fb327fec7 Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-05-23 13:06:00 +02:00
Rike
175ea9b7f9 fix version 2022-05-23 12:15:33 +02:00
SusiJo
fd31f64266
Merge branch 'master' into cnvkit_bam 2022-05-23 11:31:56 +02:00
Mahesh Binzer-Panchal
e06fb752c3
Merge branch 'master' into kat_hist 2022-05-23 08:52:13 +02:00
Rike
5d72500d60 remove variables used for test data generation, add tbi 2022-05-22 13:34:56 +02:00
Matthias De Smet
c390385cf5 revert wgsmetrics' 2022-05-22 06:44:17 +02:00
Matthias De Smet
d6a0238cd1
Merge branch 'master' into update/picard 2022-05-21 08:34:33 +02:00
Matthias De Smet
a5a6973fcf picard: make reference sequence optional 2022-05-21 08:33:49 +02:00
Ramprasad Neethiraj
635edc0022 fix typo 2022-05-20 17:07:42 +02:00
Ramprasad Neethiraj
2542c9d176 add tests 2022-05-20 16:46:19 +02:00
Mahesh Binzer-Panchal
2926ec0abb Add mash screen 2022-05-20 13:23:11 +00:00
Ramprasad Neethiraj
c70b169f61 create modules 2022-05-20 13:34:54 +02:00
SusiJo
9096be5464 improve readability 2022-05-20 13:29:49 +02:00
SusiJo
bdf222649d remove unnecessary if statement 2022-05-20 13:25:57 +02:00
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 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
Taniguti
ac7fe89a78
Merge branch 'master' into haplocheck 2022-05-13 11:24:10 -03:00
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
Taniguti
4728b2bcd2
Merge branch 'master' into haplocheck 2022-05-13 07:49:55 -03:00
Lucas Taniguti
86343cb034 feat: add haplocheck 2022-05-13 07:42:09 -03:00
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
Robert A. Petit III
8b6e1aff38
Merge branch 'master' into rp3-add-snippy 2022-05-11 12:28:27 -06:00
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
Robert A. Petit III
ef2996e4a5 match names in meta and main 2022-05-10 21:47:57 +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
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
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
7a5d5f5766
Merge branch 'master' into kat_hist 2022-05-09 13:18:18 +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
Mahesh Binzer-Panchal
1e55ad987f
Merge branch 'master' into kat_hist 2022-05-06 16:35:51 +02:00
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
nvnieuwk
5153e10840
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-06 16:19:17 +02:00
JIANHONG OU
9b50036e9b add test_bam and -m parameter for motus_profile 2022-05-06 08:56:42 -04:00
JIANHONG OU
c301a406dd
Merge branch 'nf-core:master' into motus_profile 2022-05-06 08:33:43 -04:00
Nicolas Vannieuwkerke
84b354ab6a Added the rtgtools/vcfeval module 2022-05-06 14:23:40 +02:00
JIANHONG OU
3499314b96
Update modules/motus/profile/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:19:47 -04:00
JIANHONG OU
4df57b03bd
Update modules/motus/profile/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:11:58 -04:00
JIANHONG OU
6b2f16a0f4
Update modules/motus/profile/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:11:39 -04:00
JIANHONG OU
baeb2bd1c1
Update modules/motus/profile/main.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:11:29 -04:00
JIANHONG OU
4497eb1734
Update modules/motus/profile/main.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:11:22 -04:00
Matthias De Smet
3930ba227b merge snapaligner modes into one 2022-05-06 14:10:44 +02:00
Mahesh Binzer-Panchal
9fa6b6c1fc Update meta.yml 2022-05-06 11:56:43 +00:00
Mahesh Binzer-Panchal
a9f23bb477
Merge branch 'master' into busco 2022-05-06 13:49:01 +02:00
Mahesh Binzer-Panchal
35c5828f43 Add --auto-lineage option and remove single_end 
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
 2022-05-06 11:48:21 +00:00
Jose Espinosa-Carrasco
035655e35d
Merge branch 'master' into modules/md5sum 2022-05-06 12:34:14 +02:00
Ramprasad Neethiraj
e639b1e455
Merge branch 'master' into feat/update_cnvpytor 2022-05-06 12:03:12 +02:00
Matthias De Smet
bd1b80f36e fix software definitions 2022-05-06 11:07:05 +02:00
Ramprasad Neethiraj
1ccea5ff4d remove prefix def in callcnvs 2022-05-06 10:56:58 +02:00
Matthias De Smet
1c7205d683 fixed container definitions 2022-05-06 10:44:51 +02:00
Matthias De Smet
77d825e043 fix copy paste errors 2022-05-06 10:39:13 +02:00
Matthias De Smet
09e729ad41 added sha256sum 2022-05-06 10:28:14 +02:00
Mahesh Binzer-Panchal
d83281eac9
Merge branch 'master' into kat_hist 2022-05-06 10:02:44 +02:00
Mahesh Binzer-Panchal
9194fb845e Add module kat hist 2022-05-06 07:54:10 +00:00
Matthias De Smet
853b623969 new module: md5sum 2022-05-06 09:20:40 +02:00
Ramprasad Neethiraj
313d76e005 update svdb version 2022-05-06 00:18:16 +02:00
Ramprasad Neethiraj
af73544010 update meta 2022-05-06 00:13:49 +02:00
Ramprasad Neethiraj
db56d80060 Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor 2022-05-06 00:10:28 +02:00
Ramprasad Neethiraj
e4e4f8090c combine multiple pytor 2022-05-05 23:59:12 +02:00
JIANHONG OU
e391c65510 fix the version issue for motus_profile. 2022-05-05 15:35:31 -04:00
JIANHONG OU
b8efa2ae7c
Merge branch 'master' into motus_profile 2022-05-05 13:41:54 -04:00
JIANHONG OU
fb5c5d310a update motus module. 2022-05-05 13:38:46 -04:00
Sateesh Peri
faf45edc5e
Merge branch 'master' into busco 2022-05-05 12:48:39 -04:00
Ramprasad Neethiraj
db2acba71b
Merge branch 'master' into feat/update_cnvpytor 2022-05-05 17:31:10 +02:00
Ramprasad Neethiraj
c183d7b397 Merge branch 'feat/update_cnvpytor' of github.com:ramprasadn/modules into feat/update_cnvpytor 2022-05-05 17:28:59 +02:00
Ramprasad Neethiraj
ea1f5daf44 polish python script in view 2022-05-05 17:28:49 +02:00
Harshil Patel
1289626cc9
Update modules/busco/main.nf 2022-05-05 16:09:45 +01:00
Mahesh Binzer-Panchal
2542ae1823
Update modules/busco/main.nf 
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
 2022-05-05 16:33:32 +02:00
Sateesh Peri
3414d3aba3
Merge branch 'master' into busco 2022-05-05 10:08:55 -04:00
JIANHONG OU
c8f2c44e22 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
JIANHONG OU
a8bc386ea3
Merge branch 'master' into motus_downloaddb 2022-05-05 09:36:25 -04:00
JIANHONG OU
566c11dacc
Merge branch 'master' into motus_downloaddb 2022-05-05 08:28:10 -04:00
Francesco L
97f318eea6
Merge branch 'master' into firstbranch 2022-05-05 14:25:00 +02:00
Carpanzano
a700a9c15e Merge branch 'firstbranch' of github.com:carpanz/modules into firstbranch 2022-05-05 13:52:45 +02:00
Carpanzano
9083d3bb3d integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file 2022-05-05 13:51:41 +02:00
jasmezz
47a95388c2 Remove trailing whitespaces (ECLint check) 2022-05-05 13:17:36 +02:00
jasmezz
24b9c397dd Apply suggestions from code review + add support for GFF annotations 2022-05-05 13:14:39 +02:00
MaxUlysse
40dd662fd2 update ensemblvep and snpeff modules 2022-05-05 12:57:14 +02:00
James A. Fellows Yates
e60c6f9bfd
Merge branch 'master' into firstbranch 2022-05-05 10:57:27 +02:00
Carpanzano
204dfba2d8 fixing ktupdatetaxonomy/meta.yml as suggested in PR 2022-05-05 10:51:22 +02:00
Mahesh Binzer-Panchal
865ad3447a Update meta.yml output files 2022-05-05 08:23:54 +00:00
jasmezz
6a7aec8b41 Remove prokka test workflow 2022-05-05 10:22:02 +02:00
Mahesh Binzer-Panchal
58ea709f7f
Merge branch 'master' into busco 2022-05-05 09:34:14 +02:00
James A. Fellows Yates
6393a085c5
Apply suggestions from code review 2022-05-05 08:23:51 +02:00
JIANHONG OU
29ee72c693 update meta.yml and remove the cleanup step. 2022-05-04 15:37:12 -04:00
JIANHONG OU
e9c82a5f48
Update modules/motus/downloaddb/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-04 15:29:06 -04:00
James A. Fellows Yates
35b5ba673f
Merge branch 'master' into motus_downloaddb 2022-05-04 20:58:08 +02:00
James A. Fellows Yates
ec5bada3fc
Update modules/motus/downloaddb/meta.yml 2022-05-04 20:55:16 +02:00
Lauri Mesilaakso
e757966566
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 18:41:36 +03:00
Carpanzano
a6086f549d recovered process name 2022-05-04 17:28:24 +02:00
Nicolas Vannieuwkerke
3c07602443 Added the version.yml 2022-05-04 16:51:09 +02:00
Carpanzano
8b1711d8a1 recovering old module name 2022-05-04 16:38:10 +02:00
Simone Carpanzano
162f8edf54
Merge branch 'master' into firstbranch 2022-05-04 16:35:25 +02:00
Carpanzano
6b8ca501ed fixing suggestions from PR 2022-05-04 16:34:52 +02:00
Nicolas Vannieuwkerke
f875aec46b Split the module into two parts 2022-05-04 15:29:48 +02:00
Mahesh Binzer-Panchal
5986a3efbf
Merge branch 'master' into busco 2022-05-04 15:09:54 +02:00
Nicolas Vannieuwkerke
505ab03803 fixed a description 2022-05-04 14:14:53 +02:00
Nicolas Vannieuwkerke
177a7e49f2 Fixed a linting issue 2022-05-04 14:06:42 +02:00
Nicolas Vannieuwkerke
000b8ee2e0 Merge branch 'new-module-hap.py' of github.com:nvnieuwk/modules into new-module-hap.py 2022-05-04 14:05:23 +02:00
Nicolas Vannieuwkerke
065a5d6a7f Fixed a linting issue 2022-05-04 14:05:21 +02:00
nvnieuwk
c9808cb97f
Merge branch 'master' into new-module-hap.py 2022-05-04 14:01:02 +02:00
Nicolas Vannieuwkerke
37338ecee3 Finished the module 2022-05-04 14:00:02 +02:00
Ramprasad Neethiraj
6541e151bc
Merge branch 'master' into feat/update_cnvpytor 2022-05-04 13:54:46 +02:00
Mahesh Binzer-Panchal
73a8df9522 Fix no genes found test and update test.yml 2022-05-04 11:52:42 +00:00
Nicolas Vannieuwkerke
c517ce9b4d Added the module and some simple testing 2022-05-04 13:42:12 +02:00
Mahesh Binzer-Panchal
8df20218bf Add more tests and capture summaries 
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
 2022-05-04 09:22:43 +00:00
Mahesh Binzer-Panchal
3bb0711b06
Merge branch 'master' into busco 2022-05-04 09:15:46 +02:00
Lauri Mesilaakso
530b5ac661
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 09:53:46 +03:00
Chris Cheshire
79e64cdd1f
Merge branch 'master' into expected_error_fix 2022-05-03 22:21:28 +01:00
JIANHONG OU
dc59ad0bf5 fix the version issue. 2022-05-03 12:27:39 -04:00
jasmezz
480c4ced78 Update meta.yml 2022-05-03 17:35:16 +02:00
jasmezz
fa9f0753de Apply review suggestions + add stub for prokka test workflow 2022-05-03 17:30:16 +02:00
Jill V. Hagey, PhD
f02cd618b8
Update meta.yml 2022-05-03 10:09:19 -04:00
Lauri Mesilaakso
12f79c2101
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 17:03:02 +03:00
Mahesh Binzer-Panchal
1c54c0b1ae
Apply suggestions from code review 
Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
 2022-05-03 16:02:11 +02:00
Matthieu Muffato
6351ec745e
Update contributor list 2022-05-03 14:56:27 +01:00
Matthieu Muffato
4be754b008
It's a file, not a directory 2022-05-03 14:53:17 +01:00
Mahesh Binzer-Panchal
636abad8f1
Merge branch 'master' into busco 2022-05-03 15:38:25 +02:00
Nicolas Vannieuwkerke
96d4a31cc1 Moved the BED file to the main tuple 2022-05-03 15:31:05 +02:00
Mahesh Binzer-Panchal
5f4781adaa
Merge branch 'master' into busco 2022-05-03 15:27:10 +02:00
Mahesh Binzer-Panchal
57db28386e Support batch fasta analysis 2022-05-03 13:26:49 +00:00
ljmesi
034352dbbf Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq 2022-05-03 15:18:12 +02:00
ljmesi
5510ea39fe Test --no-name to solve inconsistent checksums 2022-05-03 15:18:09 +02:00