SusiJo
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dd2f48810a
|
Merge branch 'nf-core:master' into cnvkit_bam
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2022-05-20 09:14:21 +02:00 |
|
SusiJo
|
3d57caa683
|
added test & corrected cram input
|
2022-05-20 09:13:27 +02:00 |
|
Rike
|
bb3e64647b
|
Merge remote-tracking branch 'origin/master' into gatk_filter
|
2022-05-18 15:52:47 +02:00 |
|
FriederikeHanssen
|
44e9cf56fa
|
Merge branch 'master' into gatk_cnnscore
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2022-05-18 15:32:36 +02:00 |
|
Rike
|
e8221cf98e
|
Merge remote-tracking branch 'origin' into gatk_cnnscore
|
2022-05-18 14:27:25 +02:00 |
|
James A. Fellows Yates
|
965fabdd54
|
Merge branch 'master' into motus_profile
|
2022-05-18 11:25:48 +01:00 |
|
Rike
|
5ae757121f
|
Add indices and meta
|
2022-05-17 23:38:26 +02:00 |
|
Rike
|
15fba1dd7c
|
add filter variant tranches
|
2022-05-17 23:01:24 +02:00 |
|
Rike
|
afa0f2a995
|
update test
|
2022-05-17 22:53:41 +02:00 |
|
Rike
|
265fd882ca
|
update test
|
2022-05-17 19:44:48 +02:00 |
|
Rike
|
5f63904a50
|
update test
|
2022-05-17 19:37:18 +02:00 |
|
Rike
|
e0fcbb428d
|
Add CNNScoreVariants
|
2022-05-17 19:09:46 +02:00 |
|
Jose Espinosa-Carrasco
|
3614c19206
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Merge branch 'master' into biobambam/bammerge
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2022-05-17 15:07:37 +02:00 |
|
Nicolas Vannieuwkerke
|
6342f5b099
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added bedtools split
|
2022-05-17 14:24:32 +02:00 |
|
Matthias De Smet
|
c5627e0274
|
fix config
|
2022-05-17 09:09:19 +02:00 |
|
Matthias De Smet
|
743e95c61b
|
fix config
|
2022-05-17 09:01:02 +02:00 |
|
Matthias De Smet
|
d3ddc2221a
|
Merge branch 'master' into biobambam/bammerge
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2022-05-17 08:26:28 +02:00 |
|
Matthias De Smet
|
6be91ce82d
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fix optional output detection
|
2022-05-17 08:20:47 +02:00 |
|
Subazini TK
|
79c2c529fc
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Merge branch 'master' into hmtnote
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2022-05-17 08:05:47 +02:00 |
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JIANHONG OU
|
671bacb6df
|
Merge branch 'master' into motus_profile
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2022-05-16 17:34:49 -04:00 |
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Matthias De Smet
|
d0db186e84
|
Merge branch 'master' into biobambam/bammerge
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2022-05-16 20:52:48 +02:00 |
|
Matthias De Smet
|
a79b9adeee
|
address review comments
|
2022-05-16 20:51:39 +02:00 |
|
Subazini TK
|
252fcb17c4
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
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Subazini TK
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cb21fa0c96
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
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cbae48d06d
|
Update nextflow.config
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
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541f403963
|
Update main.nf
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
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69243db3d7
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Update test.yml
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2022-05-16 15:20:15 +00:00 |
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Subazini TK
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c8c6fdd2e3
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Update main.nf
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2022-05-16 15:20:15 +00:00 |
|
Subazini TK
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fb66e8ba97
|
Update test.yml
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2022-05-16 15:20:15 +00:00 |
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Subazini TK
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f0713f4723
|
Update test.yml
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2022-05-16 15:20:15 +00:00 |
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Subazini TK
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060d33f2c3
|
Update test.yml
|
2022-05-16 15:20:15 +00:00 |
|
Subazini TK
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df8f1eae69
|
Update test.yml
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2022-05-16 15:20:15 +00:00 |
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sysbiocoder
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31fc8b560f
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hmtnote
|
2022-05-16 15:20:15 +00:00 |
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Matthias De Smet
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af69ea749d
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add module: biobambam/bammerge
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2022-05-16 14:39:58 +02:00 |
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Veit Schwämmle
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74a1c1400e
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Merge branch 'master' into maxquant
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2022-05-16 13:26:35 +02:00 |
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Jasmin F
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982c9183fa
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Merge branch 'master' into antismashlite
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2022-05-16 11:42:44 +02:00 |
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Jasmin F
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adcfae6cd4
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Merge branch 'master' into antismashlite
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2022-05-16 10:38:01 +02:00 |
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Rike
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eb841d4ea0
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revert markduplciatespark changes
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2022-05-16 10:33:01 +02:00 |
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FriederikeHanssen
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8b4d021189
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Merge branch 'master' into gatk_426
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2022-05-16 09:50:13 +02:00 |
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Matthias De Smet
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5a2e303522
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add PE sorted test
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2022-05-13 19:16:50 +02:00 |
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Matthias De Smet
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04f82d4d34
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fix test name
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2022-05-13 15:32:14 +02:00 |
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JIANHONG OU
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fadb83cf44
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Merge branch 'master' into motus_profile
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2022-05-13 09:30:20 -04:00 |
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Matthias De Smet
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cbc47767f7
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add sort option to bowtie2
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2022-05-13 15:26:41 +02:00 |
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Nicolas Vannieuwkerke
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a72f06dfe8
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removed versions checksum
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2022-05-13 14:27:59 +02:00 |
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nvnieuwk
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1d4862ba60
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Merge branch 'master' into new-module-gatk4/splitintervals
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2022-05-13 13:47:20 +02:00 |
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Nicolas Vannieuwkerke
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8a17b6dd0e
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added gatk4/splitintervals
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2022-05-13 13:46:34 +02:00 |
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Chris Cheshire
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ea55129ba3
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Removed version file checksums
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2022-05-13 12:20:41 +01:00 |
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Chris Cheshire
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9f6a1ae4a4
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Merge branch 'master' into bowtie2-test-fix
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2022-05-13 12:05:48 +01:00 |
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Chris Cheshire
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d816f2bc5d
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Reactivated all tests
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2022-05-13 12:01:16 +01:00 |
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Mahesh Binzer-Panchal
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00826dc2e9
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Merge branch 'master' into genomescope2
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2022-05-13 11:28:47 +02:00 |
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Mahesh Binzer-Panchal
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5df0bcf1be
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Update tests/modules/genomescope2/test.yml
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
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2022-05-13 11:27:42 +02:00 |
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James A. Fellows Yates
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2eebab4f35
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Update tests/modules/motus/profile/test.yml
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2022-05-12 20:55:54 +01:00 |
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James A. Fellows Yates
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8dd711aba2
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Update tests/modules/motus/profile/main.nf
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2022-05-12 20:08:37 +01:00 |
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FriederikeHanssen
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868150e1af
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Merge branch 'master' into gatk_426
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2022-05-12 19:33:07 +02:00 |
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Rike
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99880654bf
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add output default bam
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2022-05-12 18:06:15 +02:00 |
|
Rike
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8792d102ee
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fix test input
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2022-05-12 17:37:06 +02:00 |
|
Rike
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a694267b4b
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fix empty index input
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2022-05-12 17:01:03 +02:00 |
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Mahesh Binzer-Panchal
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308ab8801d
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Merge branch 'master' into kat_hist
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2022-05-12 16:52:05 +02:00 |
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Rike
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b3bd55da76
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getpileupsummaries requires intervals files
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2022-05-12 16:51:17 +02:00 |
|
Rike
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15fbf21b28
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double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere
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2022-05-12 16:16:53 +02:00 |
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Rike
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fef5434c4c
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Update md5sums
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2022-05-12 16:07:12 +02:00 |
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Jasmin F
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85b3c2bcf2
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Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-05-12 15:28:19 +02:00 |
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James A. Fellows Yates
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3c02e6056c
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Merge branch 'master' into antismashlite
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2022-05-12 14:53:52 +02:00 |
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jasmezz
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d2ef476321
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Fix Prettier linting error
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2022-05-12 12:19:50 +02:00 |
|
jasmezz
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37cc6f250b
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Fixed test.yml
|
2022-05-12 12:14:19 +02:00 |
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Chris Cheshire
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90c67794bf
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Added extra tests but error with collection
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2022-05-12 10:01:33 +01:00 |
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jasmezz
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bd4b70439b
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Streamlined some output channels, formatted tests main.nf
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2022-05-12 10:56:48 +02:00 |
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Matthias De Smet
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dcf9c07fc9
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Merge branch 'master' into update/bowtie2-align
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2022-05-11 19:08:23 +02:00 |
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Moritz E. Beber
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98d8a741ec
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tests: add missing paths to config
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2022-05-11 18:17:27 +02:00 |
|
Moritz E. Beber
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888620063b
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tests: delete settings for conda
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2022-05-11 17:44:49 +02:00 |
|
Moritz E. Beber
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b2dbaa9930
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refactor: rename module
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2022-05-11 17:33:45 +02:00 |
|
Moritz E. Beber
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23091aabda
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refactor: move files to custom section
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2022-05-11 17:33:45 +02:00 |
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Moritz E. Beber
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a83dd33a7e
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tests: use remove settings file
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2022-05-11 17:33:45 +02:00 |
|
Moritz E. Beber
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e4551a9ab3
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refactor: always output settings
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2022-05-11 17:33:45 +02:00 |
|
Moritz E. Beber
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64ff23f3c1
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feat: add module that verifies NCBI settings
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2022-05-11 17:33:45 +02:00 |
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Mahesh Binzer-Panchal
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0199d0efd2
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Merge branch 'master' into kat_hist
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2022-05-11 16:56:29 +02:00 |
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Jasmin F
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853e3ec087
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Remove commented code
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
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2022-05-11 15:56:10 +02:00 |
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Matthias De Smet
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94e8c3a882
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Update tests/modules/bowtie2/align/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2022-05-11 13:56:03 +02:00 |
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Matthias De Smet
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0d00452eca
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Update tests/modules/bowtie2/align/test.yml
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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2022-05-11 13:55:45 +02:00 |
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Matthias De Smet
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dcffd93875
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Merge branch 'master' into update/bowtie2-align
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2022-05-11 13:34:24 +02:00 |
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CMGG ICT Team
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3ae8cbfad7
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bowtie2: remove code duplication
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2022-05-11 13:32:56 +02:00 |
|
Moritz E. Beber
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0cdf7767a7
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refactor: require NCBI user settings always
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2022-05-11 13:02:52 +02:00 |
|
Moritz E. Beber
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eae7161a32
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tests: add settings input or not and test all branches
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2022-05-11 12:47:54 +02:00 |
|
Mahesh Binzer-Panchal
|
fd579ebbb3
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Merge branch 'master' into kat_hist
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2022-05-11 12:43:11 +02:00 |
|
Mahesh Binzer-Panchal
|
00fcdd0cba
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Merge branch 'master' into genomescope2
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2022-05-11 12:42:39 +02:00 |
|
Mahesh Binzer-Panchal
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d54cf467f4
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Update outputs and test data set
|
2022-05-11 10:42:17 +00:00 |
|
Harshil Patel
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7be7f404d5
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Merge branch 'master' into refactor-prefetch
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2022-05-11 11:28:02 +01:00 |
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jasmezz
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2b746abfbe
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Fix Prettier linting issue
|
2022-05-11 12:09:52 +02:00 |
|
jasmezz
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5d76f1c7ff
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Add fasta/gff input option
|
2022-05-11 12:06:02 +02:00 |
|
Jasmin F
|
9cce4a00b2
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Merge branch 'nf-core:master' into antismashlite
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2022-05-11 12:03:30 +02:00 |
|
Mahesh Binzer-Panchal
|
0774704038
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Merge branch 'master' into genomescope2
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2022-05-11 11:38:36 +02:00 |
|
Mahesh Binzer-Panchal
|
7a16ece747
|
Change md5sum to contains
|
2022-05-10 15:13:25 +00:00 |
|
Mahesh Binzer-Panchal
|
cd32c7f744
|
Merge branch 'master' into kat_hist
|
2022-05-10 17:03:00 +02:00 |
|
Mahesh Binzer-Panchal
|
9b4923dcd5
|
Change test files
|
2022-05-10 15:02:37 +00:00 |
|
Mahesh Binzer-Panchal
|
b875cfb744
|
Merge branch 'master' into kat_hist
|
2022-05-10 14:36:18 +02:00 |
|
Praveen Raj S
|
237971cd15
|
Merge branch 'master' into master
|
2022-05-10 14:35:41 +02:00 |
|
Nicolas Vannieuwkerke
|
b7134855e4
|
Small update on the output channels
|
2022-05-10 12:34:52 +02:00 |
|
Moritz E. Beber
|
1b228835e9
|
refactor: require settings input always
|
2022-05-10 12:29:42 +02:00 |
|
Moritz E. Beber
|
145e2f80e9
|
tests: run prefetch with and without given settings
|
2022-05-10 12:16:57 +02:00 |
|
Nicolas Vannieuwkerke
|
3a064b0a99
|
Split the output to different channels
|
2022-05-10 12:05:42 +02:00 |
|
Nicolas Vannieuwkerke
|
6008619603
|
test issue fix?
|
2022-05-10 10:20:54 +02:00 |
|
Nicolas Vannieuwkerke
|
96c3f895b9
|
test issue fix?
|
2022-05-10 10:19:13 +02:00 |
|
Nicolas Vannieuwkerke
|
42fbf80c72
|
Fixed a test issue with wrong md5sum
|
2022-05-10 09:57:49 +02:00 |
|
Nicolas Vannieuwkerke
|
f0e8f6ce4d
|
Linting
|
2022-05-10 09:36:54 +02:00 |
|
Nicolas Vannieuwkerke
|
e5d091ad4b
|
Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval
|
2022-05-10 09:35:44 +02:00 |
|
Nicolas Vannieuwkerke
|
c69d5cc23e
|
Added evaluation-regions and adjusted the output to now contain all output (and not only the summary)
|
2022-05-10 09:35:42 +02:00 |
|
nvnieuwk
|
95103fbd79
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-10 09:06:34 +02:00 |
|
Praveen Raj S
|
459a2d1759
|
Merge branch 'master' into master
|
2022-05-09 22:16:59 +02:00 |
|
Mahesh Binzer-Panchal
|
f65d896f57
|
create genomescope2 module
|
2022-05-09 15:09:15 +00:00 |
|
Mahesh Binzer-Panchal
|
705ad7c3a1
|
Merge branch 'master' into meryl_unionsum
|
2022-05-09 16:20:01 +02:00 |
|
nvnieuwk
|
aceb5220cf
|
Merge branch 'master' into new-module-rtg/vcfeval
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2022-05-09 16:18:00 +02:00 |
|
Mahesh Binzer-Panchal
|
83a266ea70
|
Merge branch 'master' into meryl_unionsum
|
2022-05-09 16:16:08 +02:00 |
|
FriederikeHanssen
|
adc4ff868c
|
Merge branch 'master' into samtools_convert
|
2022-05-09 16:15:24 +02:00 |
|
nvnieuwk
|
4b8bd9ebf9
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-09 15:51:31 +02:00 |
|
Mahesh Binzer-Panchal
|
da93beaf60
|
Update pytests
|
2022-05-09 13:50:49 +00:00 |
|
Nicolas Vannieuwkerke
|
f6262b4a10
|
fixed some issues
|
2022-05-09 15:47:07 +02:00 |
|
Mahesh Binzer-Panchal
|
8d86988632
|
Merge branch 'master' into meryl/histogram
|
2022-05-09 15:39:32 +02:00 |
|
nvnieuwk
|
d6dd4c2e2d
|
Update tests/modules/rtgtools/vcfeval/test.yml
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
|
2022-05-09 15:35:16 +02:00 |
|
Rike
|
ef5f145342
|
Generalize Bam2Cram do either conversion
|
2022-05-09 15:22:54 +02:00 |
|
Annick Renevey
|
ac3034696b
|
update md5sum
|
2022-05-09 15:19:16 +02:00 |
|
Mahesh Binzer-Panchal
|
f0f414d519
|
Update pytests
|
2022-05-09 13:00:10 +00:00 |
|
Annick Renevey
|
eed874ace7
|
update arriba tests
|
2022-05-09 14:55:59 +02:00 |
|
Mahesh Binzer-Panchal
|
6621768550
|
Update pytest outputs
|
2022-05-09 12:54:31 +00:00 |
|
Mahesh Binzer-Panchal
|
ce97c87b5d
|
Merge branch 'master' into meryl_unionsum
|
2022-05-09 13:51:55 +02:00 |
|
Mahesh Binzer-Panchal
|
7a5d5f5766
|
Merge branch 'master' into kat_hist
|
2022-05-09 13:18:18 +02:00 |
|
Mahesh Binzer-Panchal
|
a43bc940d6
|
Add suggestions from code review
|
2022-05-09 11:15:14 +00:00 |
|
Mahesh Binzer-Panchal
|
129f57ccd9
|
Add meryl histogram
|
2022-05-09 08:50:28 +00:00 |
|
Mahesh Binzer-Panchal
|
ad4f8389cb
|
Add meryl unionsum
|
2022-05-09 08:33:21 +00:00 |
|
Mahesh Binzer-Panchal
|
32b0fdc9d9
|
Merge branch 'master' into meryl_count
|
2022-05-09 10:05:28 +02:00 |
|
Mahesh Binzer-Panchal
|
9ebeb6a702
|
Update test
|
2022-05-09 08:05:07 +00:00 |
|
Matthias De Smet
|
3dc18365f6
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-09 10:04:29 +02:00 |
|
Mahesh Binzer-Panchal
|
4591ea2205
|
atomize
|
2022-05-09 07:58:58 +00:00 |
|
Matthias De Smet
|
2b91985aa0
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-09 09:43:48 +02:00 |
|
Nicolas Vannieuwkerke
|
d18af7358a
|
Moved untarring the genome sdf folder to the test itself
|
2022-05-09 09:20:42 +02:00 |
|
Lucpen
|
bdaed264a7
|
Merge branch 'master' into correcting_stubs
|
2022-05-09 08:54:22 +02:00 |
|
James A. Fellows Yates
|
8a83ad0518
|
Merge branch 'master' into motus_profile
|
2022-05-09 08:16:16 +02:00 |
|
Matthias De Smet
|
0752b82c9f
|
Merge branch 'master' into update/snapaligner
|
2022-05-06 18:57:37 +02:00 |
|
Matthias De Smet
|
dd458e3388
|
fix tags
|
2022-05-06 18:57:17 +02:00 |
|
Mahesh Binzer-Panchal
|
67481c6d54
|
Start Meryl count
|
2022-05-06 15:04:04 +00:00 |
|
Mahesh Binzer-Panchal
|
1e55ad987f
|
Merge branch 'master' into kat_hist
|
2022-05-06 16:35:51 +02:00 |
|
nvnieuwk
|
5153e10840
|
Merge branch 'master' into new-module-rtg/vcfeval
|
2022-05-06 16:19:17 +02:00 |
|
Lucpen
|
8e5fda3b10
|
Merge branch 'master' into correcting_stubs
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2022-05-06 15:37:08 +02:00 |
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Lucpen
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971a17a3ab
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fix datatest for stubs
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2022-05-06 15:34:18 +02:00 |
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Mahesh Binzer-Panchal
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7a85760d08
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remove 'auto' test
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2022-05-06 13:33:27 +00:00 |
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Lucpen
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0fa36e6777
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fix added correct entry workflow in test.yml
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2022-05-06 15:26:34 +02:00 |
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JIANHONG OU
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9b50036e9b
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add test_bam and -m parameter for motus_profile
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2022-05-06 08:56:42 -04:00 |
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JIANHONG OU
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c301a406dd
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Merge branch 'nf-core:master' into motus_profile
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2022-05-06 08:33:43 -04:00 |
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Nicolas Vannieuwkerke
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84b354ab6a
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Added the rtgtools/vcfeval module
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2022-05-06 14:23:40 +02:00 |
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JIANHONG OU
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26d5b4da72
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Update tests/modules/motus/profile/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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2022-05-06 08:19:54 -04:00 |
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Matthias De Smet
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3930ba227b
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merge snapaligner modes into one
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2022-05-06 14:10:44 +02:00 |
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