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Author SHA1 Message Date
Lucas Taniguti
f5615c3db6 fix: stub output name 2022-06-08 10:10:24 -03:00
Lucas Taniguti
b2afb3b2ee fix: string interpolation and test input access 2022-06-08 09:08:59 -03:00
Lucas Taniguti
abaec30889 tests: add stub 2022-06-08 08:46:22 -03:00
Lucas Taniguti
f26979c44e tests: add input to test_data.config 2022-06-08 08:10:25 -03:00
Taniguti
d5e077a2e9
Merge branch 'master' into haplocheck 2022-06-08 07:31:28 -03:00
Maxime U. Garcia
c03b8780ec
Merge pull request #1730 from FriederikeHanssen/update_tiddit 
Update TIDDIT to 3.0.0
 2022-06-08 12:23:06 +02:00
MaxUlysse
07eff4346f fix path to symbolic links 2022-06-08 11:46:45 +02:00
Maxime U. Garcia
4935bb98cb
Apply suggestions from code review 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 11:38:02 +02:00
Maxime U. Garcia
7230bf2174
Merge branch 'master' into update_tiddit 2022-06-08 11:16:01 +02:00
Taniguti
3be549534d
Apply suggestions from code review 
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
 2022-06-07 14:09:04 -03:00
Taniguti
a2e2d50494
Merge branch 'master' into haplocheck 2022-06-07 08:16:22 -03:00
nvnieuwk
f147b32fbf
Merge pull request #1733 from nvnieuwk/add-threads-to-calibratedragstrmodel 
add threads to calibratedragstrmodel
 2022-06-07 12:22:53 +02:00
Nicolas Vannieuwkerke
4c7ef30fb6 changed to label to medium 2022-06-07 12:17:14 +02:00
Nicolas Vannieuwkerke
771425e7a0 add threads to calibratedragstrmodel 2022-06-07 12:11:18 +02:00
James A. Fellows Yates
af890b1417
Merge pull request #1729 from jfy133/gatk-unifiedgenotyper 
Add gatk/unifiedgenotyper
 2022-06-03 21:31:31 +02:00
James A. Fellows Yates
d2b240a17a
Merge branch 'master' into gatk-unifiedgenotyper 2022-06-03 21:24:09 +02:00
James A. Fellows Yates
e827a042ce
Update modules/gatk/unifiedgenotyper/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-03 21:24:03 +02:00
Robert A. Petit III
b534b49b49
Merge pull request #1643 from rpetit3/rp3-add-snippy 
add module for snippy
 2022-06-03 13:20:57 -06:00
Robert A. Petit III
d7cec801b2
Update main.nf 2022-06-03 13:05:43 -06:00
Robert A. Petit III
24ca2ed464
Merge branch 'master' into rp3-add-snippy 2022-06-03 13:01:05 -06:00
MaxUlysse
97e66015ca add test + fix issues 2022-06-03 15:51:02 +02:00
MaxUlysse
f9ac4e28e9 cover all use cases 2022-06-03 15:37:10 +02:00
MaxUlysse
f1a5cc07db restructure tiddit/sv + test (just one for now) 2022-06-03 13:00:29 +02:00
MaxUlysse
40996cdbe1 update tiddit/cov + more tests 2022-06-03 12:07:16 +02:00
MaxUlysse
36ffd4fbf7 Merge remote-tracking branch 'upstream/master' into update_tiddit 2022-06-03 11:38:33 +02:00
Rike
2c9e2f5e73 Update TIDDIT to 3.0.0 2022-06-03 10:52:50 +02:00
Matthias De Smet
24403ce45d
Merge pull request #1707 from matthdsm/bump/picard 
bump picard versions
 2022-06-03 06:39:19 +02:00
Matthias De Smet
cf9d62fc83
Merge branch 'master' into bump/picard 2022-06-02 22:09:42 +02:00
James Fellows Yates
a565d9072a Add GATK UnifiedGenotyper 2022-06-02 21:39:39 +02:00
James Fellows Yates
a14855dbe8 Start meta 2022-06-02 21:22:21 +02:00
James Fellows Yates
544b62df45 Star work on GATK UG 2022-06-02 21:11:17 +02:00
nvnieuwk
fcc186d717
Merge pull request #1728 from nvnieuwk/add-intervals-to-calibratedragstrmodel 
add intervals to gatk4/calibratedragstrmodel
 2022-06-02 16:28:25 +02:00
Nicolas Vannieuwkerke
b028e57588 Merge branch 'add-intervals-to-calibratedragstrmodel' of github.com:nvnieuwk/modules into add-intervals-to-calibratedragstrmodel 2022-06-02 16:24:06 +02:00
Nicolas Vannieuwkerke
f3c0107fa2 added optional to intervals 2022-06-02 16:24:03 +02:00
nvnieuwk
897de827ee
Merge branch 'master' into add-intervals-to-calibratedragstrmodel 2022-06-02 16:20:41 +02:00
Nicolas Vannieuwkerke
b4b1f3b81d add intervals to calibratedragstrmodel 2022-06-02 16:20:12 +02:00
Maxime U. Garcia
3adb54c606
Merge pull request #1727 from maxulysse/master_ensemblvep 
update VEP version + cache
 2022-06-02 16:15:31 +02:00
MaxUlysse
b623ff5d27 fix comments 2022-06-02 16:11:45 +02:00
MaxUlysse
bc0f52bcd3 fix cache version 2022-06-02 16:11:11 +02:00
MaxUlysse
046fa39582 update VEP version + cache 2022-06-02 16:09:09 +02:00
nvnieuwk
59ce1ec348
Merge pull request #1725 from nvnieuwk/add-dragstrmodel-to-haplotypecaller 
add dragstr model to haplotypecaller
 2022-06-02 14:31:53 +02:00
nvnieuwk
e107d61069
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:20:15 +02:00
nvnieuwk
e419d306df
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:20:10 +02:00
nvnieuwk
2ce1cf3329
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:20:04 +02:00
nvnieuwk
a6c4276ad7
Update tests/modules/gatk4/haplotypecaller/test.yml 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-02 14:19:57 +02:00
Nicolas Vannieuwkerke
e53d091a6d added dragstr model to haplotypecaller 2022-06-02 14:08:09 +02:00
nvnieuwk
5447395975
Merge pull request #1724 from nvnieuwk/new-module-gatk4/CalibrateDragstrModel 
new module gatk4/calibratedragstrmodel
 2022-06-02 13:49:44 +02:00
Matthias De Smet
db0dc81b81
Merge branch 'master' into bump/picard 2022-06-02 13:49:03 +02:00
nvnieuwk
a339f9818a
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:42:56 +02:00
Matthias De Smet
22885ce687
Merge pull request #1723 from matthdsm/update/untar 
fix untar output dir
 2022-06-02 13:42:46 +02:00