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1224 commits

Author SHA1 Message Date
Thomas A. Christensen II
8b2a473f58
New module: krakentools/kreport2krona (#1746) 
* Add module definition for kreport2krona

* Add metadata for kreport2krona module

* Add tests for kreport2krona

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
 2022-06-13 20:14:44 +02:00
Maxime U. Garcia
b689b8ed88
TIDDIT - add --skip_assembly when no bwa specified (#1769) 
add --skip_assembly when no bwa specified
 2022-06-13 17:02:59 +02:00
Maxime U. Garcia
680b6c5b04
Update tiddit to 3.1.0 (#1767) 
* update TIDDIT to 3.1.0

* update VCF too as version is in file
 2022-06-13 16:24:34 +02:00
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
WackerO
f1b3174501
Merge branch 'master' into mpileup_bgzip 2022-06-13 09:48:47 +02:00
WackerO
24e05f6097
Update modules/samtools/mpileup/main.nf 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-06-13 09:35:34 +02:00
FriederikeHanssen
5b27af025a
Merge branch 'master' into manta_convert 2022-06-13 09:29:50 +02:00
FriederikeHanssen
b8ff8e32e3
Update modules/manta/convertinversion/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-13 09:26:29 +02:00
WackerO
c3b6ec8f3b Merge branch 'master' of https://github.com/nf-core/modules into mpileup_bgzip 2022-06-13 08:31:01 +02:00
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
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
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
Gisela Gabernet
5a16cf7bae
Merge branch 'master' into cellranger-7.0.0 2022-06-10 11:19:57 +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
ecf1d146ab Add full user options for AMPir 2022-06-09 16:59:00 +02:00
Maxime U. Garcia
878a5a8093
Merge branch 'master' into update_spark 2022-06-09 15:49:31 +02:00
jasmezz
ba53e09b64 Implement suggestions from code review 2022-06-09 15:37:35 +02:00
Rike
6a4732ef3b similar issues arise with bqsrspark, also use broadinstitute container 2022-06-09 15:29:00 +02:00
Rike
8e8f4c9c51 remove singulairty container 2022-06-09 15:16:11 +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
Nicolas Vannieuwkerke
81fff7384d small fix and typo 2022-06-09 15:08:02 +02:00
Rike
b9e397ff15 use broadinstitute container 2022-06-09 15:06:46 +02:00
nvnieuwk
bf73b6d376
Merge branch 'master' into new-module-gatk4/reblockgvcf 2022-06-09 14:57:20 +02:00
Nicolas Vannieuwkerke
fe9e4ece00 new module gatk4/reblockgvcf 2022-06-09 14:56:55 +02:00
Rike
ef5b0dd977 gatk4 version update to 4.2.6.1 2022-06-09 14:54:19 +02:00
nvnieuwk
e88a4ff70b
Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep 2022-06-09 11:54:22 +02:00
Nicolas Vannieuwkerke
5ccf6fbcc9 add optional fasta argument to ensemblvep 2022-06-09 11:45:27 +02:00
SusiJo
cda434611f fix conda with openjdk 1.8 2022-06-09 10:24:39 +02:00
SusiJo
0204d2374b Merge remote-tracking branch 'origin/master' into gatk_spark 2022-06-09 09:33:17 +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
Taniguti
89bffe3a5e
Merge branch 'master' into haplocheck 2022-06-08 15:00:06 -03:00