8b2a473f58
New module: krakentools/kreport2krona ( #1746 )
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* 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 )
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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 )
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* 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 )
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* 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 )
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Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-06-13 15:04:01 +02:00
Mahesh Binzer-Panchal
b036288a86
Merge pull request #1762 from mahesh-panchal/busco_md5sum_patch
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Change busco multi-fasta test md5sum to contains
2022-06-13 12:05:40 +02:00
Mahesh Binzer-Panchal
c1761293d8
Merge branch 'master' into busco_md5sum_patch
2022-06-13 10:53:36 +02:00
Mahesh Binzer-Panchal
575b2f00d3
Change busco multi-fasta test md5sum to contains
2022-06-13 08:51:41 +00:00
FriederikeHanssen
920c4e93c1
Merge pull request #1760 from WackerO/mpileup_bgzip
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Bgzip samtools/mpileup files
2022-06-13 10:49:52 +02:00
WackerO
f1b3174501
Merge branch 'master' into mpileup_bgzip
2022-06-13 09:48:47 +02:00
FriederikeHanssen
ccaf8b5f32
Merge pull request #1758 from FriederikeHanssen/manta_convert
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add manta conversion script
2022-06-13 09:42:03 +02:00
WackerO
24e05f6097
Update modules/samtools/mpileup/main.nf
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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
e5b0c7ed25
Update tests/modules/manta/convertinversion/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-13 09:26:35 +02:00
FriederikeHanssen
b8ff8e32e3
Update modules/manta/convertinversion/main.nf
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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
Taniguti
5affd97cf0
Merge pull request #1652 from lmtani/haplocheck
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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
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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
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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
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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
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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
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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
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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
