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672 commits

Author SHA1 Message Date
Merlin Szymanski
8f199c4fa4
Create atlas/splitmerge Module (#1756) 
* Add atlas/splitmerge module

* Finish the tests for atlas/splitmerge

* Prettier

* Update modules/atlas/splitmerge/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Remove curly brackets from meta.yml parameters

For single-file outputs, as reviewed

* Lintung: Remove trailing white-space

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-13 15:09:32 +02:00
Robert A. Petit III
81232af296
add module for mcroni (#1750) 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
 2022-06-13 15:04:01 +02:00
FriederikeHanssen
5b27af025a
Merge branch 'master' into manta_convert 2022-06-13 09:29:50 +02:00
Rike
650076cacf add manta conversion script 2022-06-11 13:01:18 +02:00
Taniguti
547f483b74
Merge branch 'master' into haplocheck 2022-06-10 20:39:33 -03:00
Jasmin F
7027719c67
Merge branch 'master' into r-ampir 2022-06-10 14:57:24 +02:00
Thiseas C. Lamnidis
9948e9fe21
Merge branch 'master' into sexdeterrmine 2022-06-10 11:03:18 +02:00
James A. Fellows Yates
c9db677a45
Merge branch 'master' into r-ampir 2022-06-09 19:28:37 +02:00
Nicolas Vannieuwkerke
fe9e4ece00 new module gatk4/reblockgvcf 2022-06-09 14:56:55 +02:00
James A. Fellows Yates
1fc0d3de4b
Merge branch 'gatk3-indelrealigner' into upstream-for-indel 2022-06-08 20:30:19 +02:00
James A. Fellows Yates
4a2157e5ab
Merge branch 'master' into gatk-realigntargetcreator 2022-06-08 20:15:02 +02:00
Taniguti
89bffe3a5e
Merge branch 'master' into haplocheck 2022-06-08 15:00:06 -03:00
Lucas Taniguti
f26979c44e tests: add input to test_data.config 2022-06-08 08:10:25 -03:00
Ramprasad Neethiraj
16e5e6093c Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-06-07 14:45:09 +02:00
Taniguti
a2e2d50494
Merge branch 'master' into haplocheck 2022-06-07 08:16:22 -03:00
Ramprasad Neethiraj
9d6697bdea template 2022-06-07 12:14:40 +02:00
James A. Fellows Yates
d292f822e4
Merge branch 'master' into gatk-realigntargetcreator 2022-06-03 21:33:22 +02:00
James A. Fellows Yates
d2b240a17a
Merge branch 'master' into gatk-unifiedgenotyper 2022-06-03 21:24:09 +02:00
Robert A. Petit III
24ca2ed464
Merge branch 'master' into rp3-add-snippy 2022-06-03 13:01:05 -06:00
James Fellows Yates
544b62df45 Star work on GATK UG 2022-06-02 21:11:17 +02:00
James A. Fellows Yates
abc619a3e2
Merge branch 'master' into gatk-realigntargetcreator 2022-06-02 20:24:24 +02:00
Nicolas Vannieuwkerke
e53d091a6d added dragstr model to haplotypecaller 2022-06-02 14:08:09 +02:00
nvnieuwk
a339f9818a
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:42:56 +02:00
nvnieuwk
4b430e8ece
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:41:20 +02:00
Matthias De Smet
f58771c47f
Merge branch 'master' into update/untar 2022-06-02 13:38:53 +02:00
Nicolas Vannieuwkerke
2a45d42868 added the calibratedragstrmodel module 2022-06-02 13:17:06 +02:00
Matthias De Smet
51be617b1c fix untar output dir 2022-06-02 11:09:55 +02:00
SusiJo
9fc9be3e7b Merge remote-tracking branch 'origin/master' into cnvkit_bam 2022-06-01 17:35:47 +02:00
SusiJo
f6953b5147 adjust cnvkit/batch for germline mode 2022-06-01 17:35:02 +02:00
James A. Fellows Yates
5a94794793
Merge branch 'master' into r-ampir 2022-06-01 09:18:54 +02:00
James Fellows Yates
c1ac3fbb59 Skeleton 2022-05-31 20:13:48 +02:00
Nicolas Vannieuwkerke
80366924fd added gatk4/composestrtablefile 2022-05-31 16:08:13 +02:00
James Fellows Yates
7ffe98ac8b Add gatk/indelrealigner 2022-05-30 21:12:21 +02:00
jtangrot
1c99ffd876 Add vserach usearch_global 2022-05-30 08:50:27 +02:00
Sateesh Peri
ead3679829
Merge branch 'master' into rp3-add-snippy 2022-05-26 03:04:19 -04:00
jasmezz
77b5986463 Create ampir module 2022-05-25 13:27:10 +02:00
Jill V. Hagey, PhD
b1dd1d8a52
Merge branch 'nf-core:master' into gamma-update 2022-05-24 19:28:06 -04:00
jvhagey
bb999395aa fixed pytest_modules.yml 2022-05-24 19:19:38 -04:00
Mahesh Binzer-Panchal
3d51956b88
Merge branch 'master' into kat_hist 2022-05-24 23:10:13 +02:00
Thiseas C. Lamnidis
6d04395c3c
Merge branch 'master' into sexdeterrmine 2022-05-24 13:17:37 +02:00
Mahesh Binzer-Panchal
afb5f226e6
Merge branch 'master' into kat_hist 2022-05-24 13:06:31 +02:00
Ramprasad Neethiraj
b4982ff6e3
Merge branch 'master' into rhocall 2022-05-24 09:41:30 +02:00
SusiJo
50128b0c86
Merge branch 'master' into cnvkit_reference 2022-05-24 07:49:44 +02:00
SusiJo
8fec7ae321 added new testdata path 2022-05-23 19:01:46 +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
Thiseas Christos Lamnidis
96260ced83 Add test data to config 2022-05-23 17:15:57 +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
Mahesh Binzer-Panchal
e06fb752c3
Merge branch 'master' into kat_hist 2022-05-23 08:52:13 +02:00
Rike
520dd06ca3 add new testdata 2022-05-22 13:25:39 +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
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
James A. Fellows Yates
965fabdd54
Merge branch 'master' into motus_profile 2022-05-18 11:25:48 +01:00
Rike
15fba1dd7c add filter variant tranches 2022-05-17 23:01:24 +02:00
Rike
05611cf27c update pytest 2022-05-17 19:11:05 +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
d3ddc2221a
Merge branch 'master' into biobambam/bammerge 2022-05-17 08:26:28 +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
sysbiocoder
fe009b738a modified: tests/config/pytest_modules.yml 2022-05-16 15:20:15 +00:00
Matthias De Smet
af69ea749d add module: biobambam/bammerge 2022-05-16 14:39:58 +02:00
Veit Schwämmle
74a1c1400e
Merge branch 'master' into maxquant 2022-05-16 13:26:35 +02:00
Jasmin F
adcfae6cd4
Merge branch 'master' into antismashlite 2022-05-16 10:38:01 +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
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
Taniguti
4728b2bcd2
Merge branch 'master' into haplocheck 2022-05-13 07:49:55 -03:00
Lucas Taniguti
c1ed4e21be tests: add haplocheck tests 2022-05-13 07:42:34 -03:00
Mahesh Binzer-Panchal
00826dc2e9
Merge branch 'master' into genomescope2 2022-05-13 11:28:47 +02:00
Mahesh Binzer-Panchal
308ab8801d
Merge branch 'master' into kat_hist 2022-05-12 16:52:05 +02:00
James A. Fellows Yates
3c02e6056c
Merge branch 'master' into antismashlite 2022-05-12 14:53:52 +02:00
Robert A. Petit III
8b6e1aff38
Merge branch 'master' into rp3-add-snippy 2022-05-11 12:28:27 -06:00
Moritz E. Beber
b2dbaa9930 refactor: rename module 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
Mahesh Binzer-Panchal
fbe2f85e7b Fix path 2022-05-11 13:53:38 +00:00
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
Harshil Patel
7be7f404d5
Merge branch 'master' into refactor-prefetch 2022-05-11 11:28:02 +01:00
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
44e13ae439 add module for snippy 2022-05-10 21:31:43 +00:00
Mahesh Binzer-Panchal
b875cfb744
Merge branch 'master' into kat_hist 2022-05-10 14:36:18 +02:00
Moritz E. Beber
a303904eb0 chore: add settings file to test data config 2022-05-10 12:19:25 +02:00
nvnieuwk
95103fbd79
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-10 09:06:34 +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