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966 commits

Author SHA1 Message Date
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
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
Moritz E. Beber
09bfe3c618 Apply suggestions from code review 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-10 12:16:57 +02:00
Moritz E. Beber
b1e134fdd7 docs: describe new file input 2022-05-10 12:16:57 +02:00
Moritz E. Beber
f6936e5270 refactor: accept settings as input 2022-05-10 12:16:57 +02:00
Moritz E. Beber
46a9aabfa3 chore: improve license description 2022-05-10 12:16:57 +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
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 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
James A. Fellows Yates
8a83ad0518
Merge branch 'master' into motus_profile 2022-05-09 08:16:16 +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
JIANHONG OU
b2542ee079 remove the mgc in metadata for motus_profile. 2022-05-08 06:21:26 -04:00
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
Nicolas Vannieuwkerke
eb8688d2b8 Merge branch 'new-module-rtg/vcfeval' of github.com:nvnieuwk/modules into new-module-rtg/vcfeval 2022-05-06 16:21:35 +02:00
Nicolas Vannieuwkerke
e271410017 Removed some whitespaces 2022-05-06 16:21:32 +02:00
nvnieuwk
5153e10840
Merge branch 'master' into new-module-rtg/vcfeval 2022-05-06 16:19:17 +02:00
JIANHONG OU
9b50036e9b add test_bam and -m parameter for motus_profile 2022-05-06 08:56:42 -04:00
JIANHONG OU
c301a406dd
Merge branch 'nf-core:master' into motus_profile 2022-05-06 08:33:43 -04:00
Nicolas Vannieuwkerke
84b354ab6a Added the rtgtools/vcfeval module 2022-05-06 14:23:40 +02:00
JIANHONG OU
3499314b96
Update modules/motus/profile/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:19:47 -04:00
JIANHONG OU
4df57b03bd
Update modules/motus/profile/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:11:58 -04:00
JIANHONG OU
6b2f16a0f4
Update modules/motus/profile/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:11:39 -04:00
JIANHONG OU
baeb2bd1c1
Update modules/motus/profile/main.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:11:29 -04:00
JIANHONG OU
4497eb1734
Update modules/motus/profile/main.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:11:22 -04:00
Matthias De Smet
3930ba227b merge snapaligner modes into one 2022-05-06 14:10:44 +02:00
Mahesh Binzer-Panchal
9fa6b6c1fc Update meta.yml 2022-05-06 11:56:43 +00:00
Mahesh Binzer-Panchal
a9f23bb477
Merge branch 'master' into busco 2022-05-06 13:49:01 +02:00
Mahesh Binzer-Panchal
35c5828f43 Add --auto-lineage option and remove single_end 
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
 2022-05-06 11:48:21 +00:00
Jose Espinosa-Carrasco
035655e35d
Merge branch 'master' into modules/md5sum 2022-05-06 12:34:14 +02:00
Ramprasad Neethiraj
e639b1e455
Merge branch 'master' into feat/update_cnvpytor 2022-05-06 12:03:12 +02:00
Matthias De Smet
bd1b80f36e fix software definitions 2022-05-06 11:07:05 +02:00
Ramprasad Neethiraj
1ccea5ff4d remove prefix def in callcnvs 2022-05-06 10:56:58 +02:00
Matthias De Smet
1c7205d683 fixed container definitions 2022-05-06 10:44:51 +02:00
Matthias De Smet
77d825e043 fix copy paste errors 2022-05-06 10:39:13 +02:00
Matthias De Smet
09e729ad41 added sha256sum 2022-05-06 10:28:14 +02:00
Matthias De Smet
853b623969 new module: md5sum 2022-05-06 09:20:40 +02:00
Ramprasad Neethiraj
313d76e005 update svdb version 2022-05-06 00:18:16 +02:00
Ramprasad Neethiraj
af73544010 update meta 2022-05-06 00:13:49 +02:00
Ramprasad Neethiraj
db56d80060 Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor 2022-05-06 00:10:28 +02:00
Ramprasad Neethiraj
e4e4f8090c combine multiple pytor 2022-05-05 23:59:12 +02:00
JIANHONG OU
e391c65510 fix the version issue for motus_profile. 2022-05-05 15:35:31 -04:00
JIANHONG OU
b8efa2ae7c
Merge branch 'master' into motus_profile 2022-05-05 13:41:54 -04:00
JIANHONG OU
fb5c5d310a update motus module. 2022-05-05 13:38:46 -04:00
Sateesh Peri
faf45edc5e
Merge branch 'master' into busco 2022-05-05 12:48:39 -04:00
Ramprasad Neethiraj
db2acba71b
Merge branch 'master' into feat/update_cnvpytor 2022-05-05 17:31:10 +02:00
Ramprasad Neethiraj
c183d7b397 Merge branch 'feat/update_cnvpytor' of github.com:ramprasadn/modules into feat/update_cnvpytor 2022-05-05 17:28:59 +02:00
Ramprasad Neethiraj
ea1f5daf44 polish python script in view 2022-05-05 17:28:49 +02:00
Harshil Patel
1289626cc9
Update modules/busco/main.nf 2022-05-05 16:09:45 +01:00
Mahesh Binzer-Panchal
2542ae1823
Update modules/busco/main.nf 
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
 2022-05-05 16:33:32 +02:00
Sateesh Peri
3414d3aba3
Merge branch 'master' into busco 2022-05-05 10:08:55 -04:00
JIANHONG OU
c8f2c44e22 Merge remote-tracking branch 'origin' into motus_profile 2022-05-05 09:41:13 -04:00
JIANHONG OU
a8bc386ea3
Merge branch 'master' into motus_downloaddb 2022-05-05 09:36:25 -04:00
JIANHONG OU
566c11dacc
Merge branch 'master' into motus_downloaddb 2022-05-05 08:28:10 -04:00
Francesco L
97f318eea6
Merge branch 'master' into firstbranch 2022-05-05 14:25:00 +02:00
Carpanzano
a700a9c15e Merge branch 'firstbranch' of github.com:carpanz/modules into firstbranch 2022-05-05 13:52:45 +02:00
Carpanzano
9083d3bb3d integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file 2022-05-05 13:51:41 +02:00
jasmezz
47a95388c2 Remove trailing whitespaces (ECLint check) 2022-05-05 13:17:36 +02:00
jasmezz
24b9c397dd Apply suggestions from code review + add support for GFF annotations 2022-05-05 13:14:39 +02:00
MaxUlysse
40dd662fd2 update ensemblvep and snpeff modules 2022-05-05 12:57:14 +02:00
James A. Fellows Yates
e60c6f9bfd
Merge branch 'master' into firstbranch 2022-05-05 10:57:27 +02:00
Carpanzano
204dfba2d8 fixing ktupdatetaxonomy/meta.yml as suggested in PR 2022-05-05 10:51:22 +02:00
Mahesh Binzer-Panchal
865ad3447a Update meta.yml output files 2022-05-05 08:23:54 +00:00
jasmezz
6a7aec8b41 Remove prokka test workflow 2022-05-05 10:22:02 +02:00
Mahesh Binzer-Panchal
58ea709f7f
Merge branch 'master' into busco 2022-05-05 09:34:14 +02:00
James A. Fellows Yates
6393a085c5
Apply suggestions from code review 2022-05-05 08:23:51 +02:00
JIANHONG OU
29ee72c693 update meta.yml and remove the cleanup step. 2022-05-04 15:37:12 -04:00
JIANHONG OU
e9c82a5f48
Update modules/motus/downloaddb/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-04 15:29:06 -04:00
James A. Fellows Yates
35b5ba673f
Merge branch 'master' into motus_downloaddb 2022-05-04 20:58:08 +02:00
James A. Fellows Yates
ec5bada3fc
Update modules/motus/downloaddb/meta.yml 2022-05-04 20:55:16 +02:00
Lauri Mesilaakso
e757966566
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 18:41:36 +03:00
Carpanzano
a6086f549d recovered process name 2022-05-04 17:28:24 +02:00
Nicolas Vannieuwkerke
3c07602443 Added the version.yml 2022-05-04 16:51:09 +02:00
Carpanzano
8b1711d8a1 recovering old module name 2022-05-04 16:38:10 +02:00
Simone Carpanzano
162f8edf54
Merge branch 'master' into firstbranch 2022-05-04 16:35:25 +02:00
Carpanzano
6b8ca501ed fixing suggestions from PR 2022-05-04 16:34:52 +02:00
Nicolas Vannieuwkerke
f875aec46b Split the module into two parts 2022-05-04 15:29:48 +02:00
Mahesh Binzer-Panchal
5986a3efbf
Merge branch 'master' into busco 2022-05-04 15:09:54 +02:00
Nicolas Vannieuwkerke
505ab03803 fixed a description 2022-05-04 14:14:53 +02:00
Nicolas Vannieuwkerke
177a7e49f2 Fixed a linting issue 2022-05-04 14:06:42 +02:00
Nicolas Vannieuwkerke
000b8ee2e0 Merge branch 'new-module-hap.py' of github.com:nvnieuwk/modules into new-module-hap.py 2022-05-04 14:05:23 +02:00
Nicolas Vannieuwkerke
065a5d6a7f Fixed a linting issue 2022-05-04 14:05:21 +02:00
nvnieuwk
c9808cb97f
Merge branch 'master' into new-module-hap.py 2022-05-04 14:01:02 +02:00
Nicolas Vannieuwkerke
37338ecee3 Finished the module 2022-05-04 14:00:02 +02:00
Ramprasad Neethiraj
6541e151bc
Merge branch 'master' into feat/update_cnvpytor 2022-05-04 13:54:46 +02:00
Mahesh Binzer-Panchal
73a8df9522 Fix no genes found test and update test.yml 2022-05-04 11:52:42 +00:00
Nicolas Vannieuwkerke
c517ce9b4d Added the module and some simple testing 2022-05-04 13:42:12 +02:00
Mahesh Binzer-Panchal
8df20218bf Add more tests and capture summaries 
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
 2022-05-04 09:22:43 +00:00
Mahesh Binzer-Panchal
3bb0711b06
Merge branch 'master' into busco 2022-05-04 09:15:46 +02:00
Lauri Mesilaakso
530b5ac661
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 09:53:46 +03:00
Chris Cheshire
79e64cdd1f
Merge branch 'master' into expected_error_fix 2022-05-03 22:21:28 +01:00
JIANHONG OU
dc59ad0bf5 fix the version issue. 2022-05-03 12:27:39 -04:00
jasmezz
480c4ced78 Update meta.yml 2022-05-03 17:35:16 +02:00
jasmezz
fa9f0753de Apply review suggestions + add stub for prokka test workflow 2022-05-03 17:30:16 +02:00
Jill V. Hagey, PhD
f02cd618b8
Update meta.yml 2022-05-03 10:09:19 -04:00
Lauri Mesilaakso
12f79c2101
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 17:03:02 +03:00
Mahesh Binzer-Panchal
1c54c0b1ae
Apply suggestions from code review 
Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
 2022-05-03 16:02:11 +02:00
Matthieu Muffato
6351ec745e
Update contributor list 2022-05-03 14:56:27 +01:00
Matthieu Muffato
4be754b008
It's a file, not a directory 2022-05-03 14:53:17 +01:00
Mahesh Binzer-Panchal
636abad8f1
Merge branch 'master' into busco 2022-05-03 15:38:25 +02:00
Nicolas Vannieuwkerke
96d4a31cc1 Moved the BED file to the main tuple 2022-05-03 15:31:05 +02:00
Mahesh Binzer-Panchal
5f4781adaa
Merge branch 'master' into busco 2022-05-03 15:27:10 +02:00
Mahesh Binzer-Panchal
57db28386e Support batch fasta analysis 2022-05-03 13:26:49 +00:00
ljmesi
034352dbbf Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq 2022-05-03 15:18:12 +02:00
ljmesi
5510ea39fe Test --no-name to solve inconsistent checksums 2022-05-03 15:18:09 +02:00
Ramprasad Neethiraj
26311aba2a fix minor errors 2022-05-03 15:04:37 +02:00
Ramprasad Neethiraj
be085c0173 Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor 2022-05-03 14:55:42 +02:00
Ramprasad Neethiraj
19cfb4e951 update meta files 2022-05-03 14:53:56 +02:00
Ramprasad Neethiraj
3efa931bf6 view 2022-05-03 14:26:46 +02:00
Ramprasad Neethiraj
829c15c98b partition 2022-05-03 14:26:34 +02:00
Ramprasad Neethiraj
7cc47f6ba6 importrd 2022-05-03 14:25:20 +02:00
Ramprasad Neethiraj
07e026054a histogram 2022-05-03 14:24:54 +02:00