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3013 commits 30 branches 0 tags 142 MiB
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1150 commits

Author SHA1 Message Date
Nicolas Vannieuwkerke
5ccf6fbcc9 add optional fasta argument to ensemblvep 2022-06-09 11:45:27 +02:00
James A. Fellows Yates
70f7f07a37
Apply suggestions from code review 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-06-09 08:33:37 +02:00
James Fellows Yates
939653a47e Changes after code review 2022-06-09 08:26:04 +02:00
James Fellows Yates
4d7afa21e2 Add GATK indelrealigner tests 2022-06-08 21:14:08 +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
Ramprasad Neethiraj
0b090a6b6d Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-06-08 16:34:34 +02:00
Ramprasad Neethiraj
3cabdfac20
Merge branch 'master' into update_roh 2022-06-08 15:04:34 +02:00
Ramprasad Neethiraj
c079ee2025 fix test 2022-06-08 14:48:16 +02:00
Matthias De Smet
e5f8924fab
Update modules/multiqc/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 14:41:10 +02:00
Ramprasad Neethiraj
ea4dc866e0 add index 2022-06-08 14:38:55 +02:00
Ramprasad Neethiraj
1648d2fcba add index 2022-06-08 14:36:25 +02:00
Matthias De Smet
7b018acabb
Update modules/multiqc/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 14:36:13 +02:00
Matthias De Smet
100b3f244c
Apply suggestions from code review 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 14:24:55 +02:00
Matthias De Smet
71e3056813
Merge branch 'master' into update/multiqc 2022-06-08 14:03:26 +02:00
Matthias De Smet
f1e33ca6e0 update mqc command 2022-06-08 14:02:04 +02:00
Matthias De Smet
439d2a9e67 update mqc inputs 2022-06-08 13:48:27 +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
Matthias De Smet
d196552e06 update input 2022-06-07 16:33:17 +02:00
Ramprasad Neethiraj
16e5e6093c Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-06-07 14:45:09 +02:00
Ramprasad Neethiraj
17a4e93142 fix versions.yaml 2022-06-07 14:43:35 +02:00
Ramprasad Neethiraj
65a0fb959f rhocall 2022-06-07 14:37:03 +02:00
Matthias De Smet
bffd1c562b
Merge branch 'master' into update/multiqc 2022-06-07 13:59:00 +02:00
Matthias De Smet
e5bf87aec3 possible fix for name collisions 2022-06-07 13:58:27 +02:00
Nicolas Vannieuwkerke
4c7ef30fb6 changed to label to medium 2022-06-07 12:17:14 +02:00
Ramprasad Neethiraj
9d6697bdea template 2022-06-07 12:14:40 +02:00
Nicolas Vannieuwkerke
771425e7a0 add threads to calibratedragstrmodel 2022-06-07 12:11:18 +02:00
James A. Fellows Yates
0d087b4890
Update modules/gatk/realignertargetcreator/main.nf 2022-06-03 21:33:54 +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
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
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
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
James Fellows Yates
de88adc926 Standardise parameters (no tests yet until realigntarget creator ready) 2022-06-02 20:35:34 +02:00
James Fellows Yates
9a4f22e8d1 Merge branch 'gatk-realigntargetcreator' of github.com:jfy133/nf-core-modules into gatk-realigntargetcreator 2022-06-02 20:32:03 +02:00
James Fellows Yates
c469a2b35e Fux tests 2022-06-02 20:32:00 +02:00
James Fellows Yates
599b264280 Standaridse parameters 2022-06-02 20:27:16 +02:00
James A. Fellows Yates
b1edcc6e94
Update modules/gatk/realignertargetcreator/main.nf 2022-06-02 20:26:09 +02:00