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Author SHA1 Message Date
WackerO
c3b6ec8f3b Merge branch 'master' of https://github.com/nf-core/modules into mpileup_bgzip 2022-06-13 08:31:01 +02:00
Taniguti
5affd97cf0
Merge pull request #1652 from lmtani/haplocheck 
Add Haplocheck
 2022-06-11 08:50:24 -03:00
WackerO
dc6c09e083 samtools mpileup now bgzips mpileup files 2022-06-11 13:32:53 +02:00
Rike
dd6c514710 Fix linting 2022-06-11 13:12:56 +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
James A. Fellows Yates
ab422e54b5
Merge pull request #1697 from jasmezz/r-ampir 
Add ampir
 2022-06-10 15:11:49 +02:00
Jasmin F
7027719c67
Merge branch 'master' into r-ampir 2022-06-10 14:57:24 +02:00
James A. Fellows Yates
01d4a1fa3a
Apply suggestions from code review 2022-06-10 14:46:58 +02:00
Mahesh Binzer-Panchal
afed00fb62
Merge pull request #1753 from mahesh-panchal/allow_git_sha_versions 
Allow Git commit SHA's as version numbers
 2022-06-10 13:32:21 +02:00
Mahesh Binzer-Panchal
f8bd7902d9 Update Git SHA messagre 2022-06-10 11:01:40 +00:00
Mahesh Binzer-Panchal
25c742dc69 Commit suggestions from code review 2022-06-10 10:56:56 +00:00
jasmezz
088b5b14f6 Merge branch 'r-ampir' of github.com:jasmezz/modules into r-ampir 2022-06-10 12:54:47 +02:00
jasmezz
39388abc04 Add file name collision check + TSV output 2022-06-10 12:54:39 +02:00
Mahesh Binzer-Panchal
6a1cbce0f5
Update tests/test_versions_yml.py 
Co-authored-by: Fabian Egli <fabianegli@users.noreply.github.com>
 2022-06-10 12:54:08 +02:00
Mahesh Binzer-Panchal
e75dd10667
Merge branch 'master' into allow_git_sha_versions 2022-06-10 12:53:50 +02:00
Alexander Peltzer
f7b2314ec4
Merge pull request #1751 from nf-core/cellranger-7.0.0 
CellRanger 7.0.0 / Apart from cconda, all is green 🥳
 2022-06-10 12:02:30 +02:00
Alexander Peltzer
a0747b1405 Remove empty file md5sum 2022-06-10 11:53:28 +02:00
Alexander Peltzer
63f47551a8 Fix empty test having md5sum 2022-06-10 11:52:30 +02:00
Alexander Peltzer
1fbe69cfcc Updated and fixed tests 2022-06-10 11:46:23 +02:00
Mahesh Binzer-Panchal
0479544e02 Allow Git commit SHA's as version numbers 2022-06-10 09:46:14 +00:00
Alexander Peltzer
8dfe8b795f Merge remote-tracking branch 'refs/remotes/origin/cellranger-7.0.0' into cellranger-7.0.0 2022-06-10 11:23:15 +02:00
Alexander Peltzer
4928dfad34 Trying to fix tests 2022-06-10 11:22:45 +02:00
Alexander Peltzer
570a43ba4c Fix tests 2022-06-10 11:21:03 +02:00
Gisela Gabernet
5a16cf7bae
Merge branch 'master' into cellranger-7.0.0 2022-06-10 11:19:57 +02:00
Thiseas C. Lamnidis
8553388c17
Merge pull request #1687 from TCLamnidis/sexdeterrmine 
Add sexdeterrmine module
 2022-06-10 11:10:51 +02:00
Alexander Peltzer
62c4b59d10
Update main.nf 2022-06-10 11:05:59 +02:00
Thiseas C. Lamnidis
9948e9fe21
Merge branch 'master' into sexdeterrmine 2022-06-10 11:03:18 +02:00
Thiseas C. Lamnidis
fe855a1c23
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-10 11:03:01 +02:00
Alexander Peltzer
cfcd93f3e7
Update Dockerfile 2022-06-10 10:56:13 +02:00
Alexander Peltzer
61d87bb2bc
Update main.nf 2022-06-10 10:54:06 +02:00
Alexander Peltzer
e499abe572
Update main.nf 2022-06-10 10:53:48 +02:00
Alexander Peltzer
8032833e6e
Update main.nf 2022-06-10 10:53:09 +02:00
Alexander Peltzer
e36b79201d
Update Dockerfile 2022-06-10 10:52:13 +02:00
James A. Fellows Yates
c9db677a45
Merge branch 'master' into r-ampir 2022-06-09 19:28:37 +02:00
jasmezz
5841f11edb Replace MD5 with contains check 2022-06-09 18:15:27 +02:00
jasmezz
ecf1d146ab Add full user options for AMPir 2022-06-09 16:59:00 +02:00
FriederikeHanssen
a427bd587f
Merge pull request #1743 from FriederikeHanssen/update_spark 
gatk4 version update to 4.2.6.1
 2022-06-09 16:06:44 +02:00
Maxime U. Garcia
878a5a8093
Merge branch 'master' into update_spark 2022-06-09 15:49:31 +02:00
Rike
30262d1fdd remove variable checksum 2022-06-09 15:44:12 +02:00
Rike
a5583143c4 update checksum 2022-06-09 15:38:28 +02:00
jasmezz
ba53e09b64 Implement suggestions from code review 2022-06-09 15:37:35 +02:00
Rike
95633c6853 update checksum 2022-06-09 15:30:47 +02:00
Rike
6a4732ef3b similar issues arise with bqsrspark, also use broadinstitute container 2022-06-09 15:29:00 +02:00
nvnieuwk
2becc8471b
Merge pull request #1744 from nvnieuwk/new-module-gatk4/reblockgvcf 
new module gatk4/reblockgvcf
 2022-06-09 15:20:18 +02:00
Rike
8e8f4c9c51 remove singulairty container 2022-06-09 15:16:11 +02:00
Nicolas Vannieuwkerke
62803e774e Merge branch 'new-module-gatk4/reblockgvcf' of github.com:nvnieuwk/modules into new-module-gatk4/reblockgvcf 2022-06-09 15:14:39 +02:00
Nicolas Vannieuwkerke
c50df9ad04 fix test.yml 2022-06-09 15:14:37 +02:00
nvnieuwk
873215c8ae
Update modules/gatk4/reblockgvcf/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-09 15:11:18 +02:00
Rike
89a6a03e38 fix container tag 2022-06-09 15:09:19 +02:00