Commit graph

816 commits

Author SHA1 Message Date
jasmezz
bd4b70439b Streamlined some output channels, formatted tests main.nf 2022-05-12 10:56:48 +02:00
Jasmin F
853e3ec087
Remove commented code
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-05-11 15:56:10 +02:00
jasmezz
5d76f1c7ff Add fasta/gff input option 2022-05-11 12:06:02 +02:00
Jasmin F
9cce4a00b2
Merge branch 'nf-core:master' into antismashlite 2022-05-11 12:03:30 +02:00
Praveen Raj S
237971cd15
Merge branch 'master' into master 2022-05-10 14:35:41 +02:00
Nicolas Vannieuwkerke
fa7c947c35 Adjusted meta 2022-05-10 13:33:37 +02:00
Nicolas Vannieuwkerke
b7134855e4 Small update on the output channels 2022-05-10 12:34:52 +02:00
Nicolas Vannieuwkerke
c18391aa49 Updated meta.yml 2022-05-10 12:26:13 +02:00
nvnieuwk
2eb77bd64e
Update modules/rtgtools/vcfeval/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-05-10 12:22:56 +02:00
nvnieuwk
29f2d3c284
Update modules/rtgtools/vcfeval/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-05-10 12:22:49 +02:00
Nicolas Vannieuwkerke
ef4857ec54 Updated meta.yml 2022-05-10 12:20:01 +02:00
Nicolas Vannieuwkerke
f3d5584ab0 Linting 2022-05-10 12:08:23 +02:00
Nicolas Vannieuwkerke
5db26f9f35 Linting 2022-05-10 12:07:11 +02:00
Nicolas Vannieuwkerke
3a064b0a99 Split the output to different channels 2022-05-10 12:05:42 +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
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 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
Rike
da79396f06 rename aligned to alignment 2022-05-09 16:07:49 +02:00
Rike
5bd456e5e8 rename file_type to output extension 2022-05-09 16:06:22 +02:00
Rike
1de1c2253e Combine output after code review 2022-05-09 16:04:58 +02:00
Nicolas Vannieuwkerke
bd7e1414a4 Fixed meta.yml 2022-05-09 15:55:48 +02:00
nvnieuwk
4b8bd9ebf9
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-09 15:51:31 +02:00
Nicolas Vannieuwkerke
1b63d03f8e adjusted the bed variable name 2022-05-09 15:51:19 +02:00
Nicolas Vannieuwkerke
f6262b4a10 fixed some issues 2022-05-09 15:47:07 +02:00
Rike
24d5e7feed Code review suggestions 2022-05-09 15:42:55 +02:00
Mahesh Binzer-Panchal
8d86988632
Merge branch 'master' into meryl/histogram 2022-05-09 15:39:32 +02:00
Rike
ef5f145342 Generalize Bam2Cram do either conversion 2022-05-09 15:22:54 +02:00
Mahesh Binzer-Panchal
57fee2b3d6 Add description pattern 2022-05-09 12:56:22 +00:00
Annick Renevey
bf91f9dd9b update arriba module 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
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
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
nvnieuwk
6fd9246aef
Update modules/rtgtools/vcfeval/main.nf
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-05-09 08:07:33 +02:00
Harshil Patel
2676f8eef4
Merge branch 'master' into fix-prefetch 2022-05-06 19:33:44 +01:00
Matthias De Smet
0752b82c9f
Merge branch 'master' into update/snapaligner 2022-05-06 18:57:37 +02:00
Moritz E. Beber
ea41c753c0 fix: remove retry label
Call gets retried by bash script
2022-05-06 17:28:56 +02:00
Moritz E. Beber
dd1c66783a refactor: use a template to add retrying 2022-05-06 17:26:41 +02:00
Moritz E. Beber
ed09978222 chore: update build number 2022-05-06 17:26:41 +02:00
Mahesh Binzer-Panchal
67481c6d54 Start Meryl count 2022-05-06 15:04:04 +00:00