Jasmin F
982c9183fa
Merge branch 'master' into antismashlite
2022-05-16 11:42:44 +02:00
Jasmin F
adcfae6cd4
Merge branch 'master' into antismashlite
2022-05-16 10:38:01 +02:00
Rike
eb841d4ea0
revert markduplciatespark changes
2022-05-16 10:33:01 +02:00
FriederikeHanssen
8b4d021189
Merge branch 'master' into gatk_426
2022-05-16 09:50:13 +02:00
Matthias De Smet
5a2e303522
add PE sorted test
2022-05-13 19:16:50 +02:00
Taniguti
ac7fe89a78
Merge branch 'master' into haplocheck
2022-05-13 11:24:10 -03:00
Matthias De Smet
04f82d4d34
fix test name
2022-05-13 15:32:14 +02:00
JIANHONG OU
fadb83cf44
Merge branch 'master' into motus_profile
2022-05-13 09:30:20 -04:00
Matthias De Smet
cbc47767f7
add sort option to bowtie2
2022-05-13 15:26:41 +02:00
Nicolas Vannieuwkerke
a72f06dfe8
removed versions checksum
2022-05-13 14:27:59 +02:00
nvnieuwk
1d4862ba60
Merge branch 'master' into new-module-gatk4/splitintervals
2022-05-13 13:47:20 +02:00
Nicolas Vannieuwkerke
8a17b6dd0e
added gatk4/splitintervals
2022-05-13 13:46:34 +02:00
Chris Cheshire
ea55129ba3
Removed version file checksums
2022-05-13 12:20:41 +01:00
Chris Cheshire
9f6a1ae4a4
Merge branch 'master' into bowtie2-test-fix
2022-05-13 12:05:48 +01:00
Chris Cheshire
d816f2bc5d
Reactivated all tests
2022-05-13 12:01:16 +01:00
Taniguti
4728b2bcd2
Merge branch 'master' into haplocheck
2022-05-13 07:49:55 -03:00
Lucas Taniguti
c1ed4e21be
tests: add haplocheck tests
2022-05-13 07:42:34 -03:00
Mahesh Binzer-Panchal
00826dc2e9
Merge branch 'master' into genomescope2
2022-05-13 11:28:47 +02:00
Mahesh Binzer-Panchal
5df0bcf1be
Update tests/modules/genomescope2/test.yml
...
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-13 11:27:42 +02:00
James A. Fellows Yates
2eebab4f35
Update tests/modules/motus/profile/test.yml
2022-05-12 20:55:54 +01:00
James A. Fellows Yates
8dd711aba2
Update tests/modules/motus/profile/main.nf
2022-05-12 20:08:37 +01:00
FriederikeHanssen
868150e1af
Merge branch 'master' into gatk_426
2022-05-12 19:33:07 +02:00
Rike
99880654bf
add output default bam
2022-05-12 18:06:15 +02:00
Rike
8792d102ee
fix test input
2022-05-12 17:37:06 +02:00
Rike
a694267b4b
fix empty index input
2022-05-12 17:01:03 +02:00
Mahesh Binzer-Panchal
308ab8801d
Merge branch 'master' into kat_hist
2022-05-12 16:52:05 +02:00
Rike
b3bd55da76
getpileupsummaries requires intervals files
2022-05-12 16:51:17 +02:00
Rike
15fbf21b28
double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere
2022-05-12 16:16:53 +02:00
Rike
fef5434c4c
Update md5sums
2022-05-12 16:07:12 +02:00
Jasmin F
85b3c2bcf2
Apply suggestions from code review
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-12 15:28:19 +02:00
James A. Fellows Yates
3c02e6056c
Merge branch 'master' into antismashlite
2022-05-12 14:53:52 +02:00
Sateesh Peri
c5d3c90524
Merge branch 'master' into rp3-add-snippy
2022-05-12 07:48:33 -04:00
jasmezz
d2ef476321
Fix Prettier linting error
2022-05-12 12:19:50 +02:00
jasmezz
37cc6f250b
Fixed test.yml
2022-05-12 12:14:19 +02:00
Chris Cheshire
90c67794bf
Added extra tests but error with collection
2022-05-12 10:01:33 +01:00
jasmezz
bd4b70439b
Streamlined some output channels, formatted tests main.nf
2022-05-12 10:56:48 +02:00
Robert A. Petit III
8b6e1aff38
Merge branch 'master' into rp3-add-snippy
2022-05-11 12:28:27 -06:00
Robert A. Petit III
7ced6e20de
make prettier
2022-05-11 18:00:36 +00:00
Moritz E. Beber
74b11ccc44
refactor: rename and update subworkflow
2022-05-11 19:24:16 +02:00
Matthias De Smet
dcf9c07fc9
Merge branch 'master' into update/bowtie2-align
2022-05-11 19:08:23 +02:00
Moritz E. Beber
98d8a741ec
tests: add missing paths to config
2022-05-11 18:17:27 +02:00
Moritz E. Beber
888620063b
tests: delete settings for conda
2022-05-11 17:44:49 +02:00
Moritz E. Beber
b2dbaa9930
refactor: rename module
2022-05-11 17:33:45 +02:00
Moritz E. Beber
23091aabda
refactor: move files to custom section
2022-05-11 17:33:45 +02:00
Moritz E. Beber
a83dd33a7e
tests: use remove settings file
2022-05-11 17:33:45 +02:00
Moritz E. Beber
e4551a9ab3
refactor: always output settings
2022-05-11 17:33:45 +02:00
Moritz E. Beber
64ff23f3c1
feat: add module that verifies NCBI settings
2022-05-11 17:33:45 +02:00
Mahesh Binzer-Panchal
0199d0efd2
Merge branch 'master' into kat_hist
2022-05-11 16:56:29 +02:00
Harshil Patel
4e603393c3
Merge branch 'master' into update/bowtie2-align
2022-05-11 15:47:37 +01:00
Jasmin F
853e3ec087
Remove commented code
...
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2022-05-11 15:56:10 +02:00
Mahesh Binzer-Panchal
fbe2f85e7b
Fix path
2022-05-11 13:53:38 +00:00
Matthias De Smet
94e8c3a882
Update tests/modules/bowtie2/align/test.yml
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-05-11 13:56:03 +02:00
Matthias De Smet
0d00452eca
Update tests/modules/bowtie2/align/test.yml
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-05-11 13:55:45 +02:00
Matthias De Smet
dcffd93875
Merge branch 'master' into update/bowtie2-align
2022-05-11 13:34:24 +02:00
CMGG ICT Team
3ae8cbfad7
bowtie2: remove code duplication
2022-05-11 13:32:56 +02:00
Moritz E. Beber
0cdf7767a7
refactor: require NCBI user settings always
2022-05-11 13:02:52 +02:00
Moritz E. Beber
eae7161a32
tests: add settings input or not and test all branches
2022-05-11 12:47:54 +02:00
Mahesh Binzer-Panchal
fd579ebbb3
Merge branch 'master' into kat_hist
2022-05-11 12:43:11 +02:00
Mahesh Binzer-Panchal
00fcdd0cba
Merge branch 'master' into genomescope2
2022-05-11 12:42:39 +02:00
Mahesh Binzer-Panchal
d54cf467f4
Update outputs and test data set
2022-05-11 10:42:17 +00:00
Harshil Patel
7be7f404d5
Merge branch 'master' into refactor-prefetch
2022-05-11 11:28:02 +01:00
jasmezz
2b746abfbe
Fix Prettier linting issue
2022-05-11 12:09:52 +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
Mahesh Binzer-Panchal
0774704038
Merge branch 'master' into genomescope2
2022-05-11 11:38:36 +02:00
Robert A. Petit III
56e94f625e
remove empty file md5
2022-05-10 21:47:11 +00:00
Robert A. Petit III
44e13ae439
add module for snippy
2022-05-10 21:31:43 +00:00
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
a303904eb0
chore: add settings file to test data config
2022-05-10 12:19:25 +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
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
0c567f5474
Merge branch 'master' into meryl_unionsum
2022-05-09 15:03:27 +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
Jasmin F
453d5b66a4
Add Bacteroides fragilis GFF file
2022-05-09 14:46:18 +02:00
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
MaxUlysse
3d428e2933
fix spacing
2022-05-07 15:28:40 +02:00
MaxUlysse
1013be2623
fix path to script
2022-05-07 15:22:52 +02:00
Jose Espinosa-Carrasco
e2acf28c8f
Merge branch 'master' into maxulysse-patch-1
2022-05-06 23:53:27 +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
Maxime U. Garcia
ac217479e9
Update tests/config/test_data.config
...
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-05-06 18:18:32 +02:00
Maxime U. Garcia
ec7b460fa4
add missing file
2022-05-06 17:54:35 +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
Nicolas Vannieuwkerke
8c857dee3a
Fixed the sdf folder fetching
2022-05-06 16:16:57 +02:00
Lucpen
8e5fda3b10
Merge branch 'master' into correcting_stubs
2022-05-06 15:37:08 +02:00
Lucpen
971a17a3ab
fix datatest for stubs
2022-05-06 15:34:18 +02:00
Mahesh Binzer-Panchal
7a85760d08
remove 'auto' test
2022-05-06 13:33:27 +00:00
Lucpen
0fa36e6777
fix added correct entry workflow in test.yml
2022-05-06 15:26:34 +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
26d5b4da72
Update tests/modules/motus/profile/main.nf
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-06 08:19:54 -04:00
Matthias De Smet
26d2231e85
fix linting
2022-05-06 14:16:38 +02:00
Matthias De Smet
3930ba227b
merge snapaligner modes into one
2022-05-06 14:10:44 +02:00
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
Mahesh Binzer-Panchal
c19e7da59d
Apply suggestions from code review
...
Remove versions md5sum
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-05-06 10:55:48 +02:00
Matthias De Smet
09e729ad41
added sha256sum
2022-05-06 10:28:14 +02:00
Mahesh Binzer-Panchal
d83281eac9
Merge branch 'master' into kat_hist
2022-05-06 10:02:44 +02:00
Mahesh Binzer-Panchal
9194fb845e
Add module kat hist
2022-05-06 07:54:10 +00:00
Matthias De Smet
853b623969
new module: md5sum
2022-05-06 09:20:40 +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
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
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
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
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
ljmesi
888e122f05
Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq
2022-05-05 08:32:48 +02:00
ljmesi
be8ce6de2a
Remove variable md5sum from the tests
2022-05-05 08:32:45 +02:00
James A. Fellows Yates
35b5ba673f
Merge branch 'master' into motus_downloaddb
2022-05-04 20:58:08 +02:00
Lauri Mesilaakso
e757966566
Merge branch 'master' into add_compression_to_bam2fq
2022-05-04 18:41:36 +03:00
Carpanzano
38faf040ec
missing change in ext.args config
2022-05-04 16:54:15 +02:00
Nicolas Vannieuwkerke
3c07602443
Added the version.yml
2022-05-04 16:51:09 +02:00
Carpanzano
e7b92a7616
fixing md5sum changes
2022-05-04 16:43:22 +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
42bdc5471e
Changed the pytest location of happy
2022-05-04 15:40:34 +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
3c66138672
Linting issue + removed the contains lines
2022-05-04 14:49:17 +02:00
Nicolas Vannieuwkerke
5889d6c923
Another possible fix for the pytest issues
2022-05-04 14:46:15 +02:00
Nicolas Vannieuwkerke
583ea13800
Another try to fix the pytest issues
2022-05-04 14:22:55 +02:00
Nicolas Vannieuwkerke
17dbd2bb82
Linting issue fixed
2022-05-04 14:18:56 +02:00
Nicolas Vannieuwkerke
c1393bf999
Possible fix for the pytest errors?
2022-05-04 14:14:01 +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
Mahesh Binzer-Panchal
f65abe1e9a
Prettier
2022-05-04 11:54:51 +00:00
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
jasmezz
fa9f0753de
Apply review suggestions + add stub for prokka test workflow
2022-05-03 17:30:16 +02:00
Lauri Mesilaakso
12f79c2101
Merge branch 'master' into add_compression_to_bam2fq
2022-05-03 17:03:02 +03:00
ljmesi
a39fa4e003
Fix checksum for one file
2022-05-03 15:47:49 +02:00
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
46e5752b82
update tests
2022-05-03 14:32:45 +02:00
Lauri Mesilaakso
a65e76e3dd
Merge branch 'master' into add_compression_to_bam2fq
2022-05-03 14:30:54 +03:00
Chris Cheshire
6f35537d40
Merge branch 'master' into expected_error_fix
2022-05-03 12:21:51 +01:00
Chris Cheshire
829183ee84
Merge branch 'master' into rp3-add-shigatyper
2022-05-03 12:16:54 +01:00
Chris Cheshire
6015478b72
Merge branch 'master' into add-slimfastq
2022-05-03 12:11:19 +01:00
Chris Cheshire
d7fb969a74
Merge branch 'master' into rp3-add-shigatyper
2022-05-03 12:10:23 +01:00
Chris Cheshire
40e6bd9dc1
bowtie2|fix tags error
2022-05-03 12:07:04 +01:00
Chris Cheshire
0f1ee7e50d
bowtie2|test fixes
2022-05-03 12:04:51 +01:00
Chris Cheshire
61f68913fe
Merge branch 'master' into expected_error_fix
2022-05-03 11:49:35 +01:00
Chris Cheshire
768073be63
bowtie2|Added support for large indexes
2022-05-03 11:46:19 +01:00
Mahesh Binzer-Panchal
ddbe6e8f40
Merge branch 'master' into busco
2022-05-03 10:48:03 +02:00
Mahesh Binzer-Panchal
9a72548ee1
Update busco module
2022-05-03 08:42:56 +00:00
Lauri Mesilaakso
6367c6a1ad
Merge branch 'master' into add_compression_to_bam2fq
2022-05-03 11:41:25 +03:00
nvnieuwk
f85787b19e
Merge branch 'master' into vardict-java
2022-05-03 10:17:04 +02:00
Lauri Mesilaakso
773e6f8e93
Merge branch 'master' into add_compression_to_bam2fq
2022-05-03 11:13:55 +03:00
ljmesi
59d6e6e1dd
Add updated md5sums
2022-05-03 09:56:50 +02:00
Ramprasad Neethiraj
6f787aea71
Merge branch 'master' into adding_stub_to_modules
2022-05-03 09:43:16 +02:00
Nicolas Vannieuwkerke
9127f92ddd
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-05-03 08:29:50 +02:00
Nicolas Vannieuwkerke
9a10e5beb5
Added the missing inputs in meta.yml + correct notation
2022-05-03 08:29:46 +02:00
Matthias De Smet
1687bfcb85
Merge branch 'master' into add-slimfastq
2022-05-03 08:22:49 +02:00
Matthias De Smet
a67c06af81
Merge branch 'master' into vardict-java
2022-05-03 08:22:19 +02:00
Jill V. Hagey, PhD
23cfb5dd42
Update test.yml
2022-05-02 18:38:48 -04:00
Jill V. Hagey, PhD
db9681029c
Update test.yml
2022-05-02 18:27:01 -04:00
Jill V. Hagey, PhD
7b0d6f96fd
Update test.yml
2022-05-02 18:20:54 -04:00
Jill V. Hagey, PhD
e5d7c80bb5
Update test.yml
2022-05-02 18:13:14 -04:00
Moritz E. Beber
16aa3915e3
feat: add module for slimfastq
2022-05-02 23:16:59 +02:00
Carpanzano
d2e1408b0f
updated content for html file in test yml
2022-05-02 18:44:05 +02:00
carpanz
e8b2445878
updated file location in test yml
2022-05-02 18:43:20 +02:00
Carpanzano
1deb789502
synced withName ext.args with process name
2022-05-02 18:39:45 +02:00
Carpanzano
5136ed29c4
removed include and changed process name due to expected folder name before tokenize
2022-05-02 18:38:59 +02:00
Ramprasad Neethiraj
3194729f82
Merge branch 'master' into adding_stub_to_modules
2022-05-02 18:31:55 +02:00
Jill V. Hagey, PhD
99a8711997
Update tests/modules/srst2/srst2/test.yml
...
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-05-02 12:26:56 -04:00
Carpanzano
32b8f3f612
adding contain for html output in test yml
2022-05-02 18:21:26 +02:00
carpanz
6e83196634
updating test yml after removing kronadb from test
2022-05-02 18:20:36 +02:00
Carpanzano
b0a2d36ec1
removing kronadb module from testing ktimporttaxonomy test - NB: temporarily using test db while testdb is added to test-datasets
2022-05-02 18:16:08 +02:00
Sateesh Peri
c56b371713
Merge branch 'master' into srst2/srst2
2022-05-02 12:13:11 -04:00
jasmezz
a992a0207e
Merge branch 'antismashlite' of github.com:jasmezz/modules into antismashlite
2022-05-02 17:58:52 +02:00
Jasmin F
b8386c42a7
Merge branch 'nf-core:master' into antismashlite
2022-05-02 17:58:19 +02:00
jasmezz
d19e65d2a2
Merge branch 'antismashlite' of github.com:jasmezz/modules into antismashlite
2022-05-02 17:56:23 +02:00
jasmezz
35cc8152b8
Fix missing test input
2022-05-02 17:55:39 +02:00
Simone Carpanzano
3d9c8a6bb1
Merge branch 'master' into firstbranch
2022-05-02 17:43:33 +02:00
Carpanzano
c9ab26ba8e
synced name of report as in test config
2022-05-02 17:41:55 +02:00
Carpanzano
76a0e3ef04
updated config kraken report name
2022-05-02 17:40:50 +02:00
jvhagey
cd45dc1550
linting test.yml
2022-05-02 11:38:39 -04:00
Jasmin F
883b95bed6
Merge branch 'nf-core:master' into antismashlite
2022-05-02 17:31:43 +02:00
jasmezz
4a4de550b8
Simplify/reduce container mount volumes
2022-05-02 17:30:46 +02:00
jvhagey
24dc2d2113
added tests
2022-05-02 11:30:19 -04:00
Carpanzano
1188264fa2
finished test yml file
2022-05-02 17:25:58 +02:00
carpanz
028dc3cb87
updated test yml file
2022-05-02 17:24:55 +02:00
Carpanzano
3cebcbfc0a
remove taxonomy not used in place of db
2022-05-02 17:13:58 +02:00
Carpanzano
2e4c200a26
remove new line between includes
2022-05-02 17:13:20 +02:00
Jasmin F
235944f797
Merge branch 'master' into antismash_db_output
2022-05-02 17:11:51 +02:00
Carpanzano
700d6ab3f1
errore TDOWNLOAD
2022-05-02 16:55:18 +02:00
Carpanzano
80f107515e
update nextflow.config withName
2022-05-02 16:22:22 +02:00
Carpanzano
42310cbce2
updated config to reflect names in test workflow
2022-05-02 16:14:38 +02:00
Carpanzano
38d9d81aaf
update code
2022-05-02 16:10:57 +02:00
Lucpen
50cc136a78
Update tests/modules/gatk4/mutect2/main.nf
...
fix spelling mistake
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-05-02 15:14:05 +02:00
JIANHONG OU
b14f30936e
Merge branch 'nf-core:master' into motus_downloaddb
2022-05-02 08:42:09 -04:00
JIANHONG OU
0f24e4dcff
add input database and intermediate bam file.
2022-05-02 08:37:12 -04:00
Lucpen
dfabf960dc
Merge branch 'master' into adding_stub_to_modules
2022-05-02 14:20:03 +02:00
JIANHONG OU
3f07761da5
remove the output check for the versions.yml.
2022-05-02 08:19:13 -04:00
Lucpen
da82e06354
fix gatk4_mutect2 test
2022-05-02 14:16:07 +02:00
Lucpen
3a4e415fe2
chores adding dummy files for stubs
2022-05-02 13:30:18 +02:00
James A. Fellows Yates
f1c2f624eb
Update tests/modules/diamond/blastx/main.nf
...
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
2022-05-02 13:17:22 +02:00
Lucpen
de40c1bf54
chore removing file from test
2022-05-02 13:15:01 +02:00
James Fellows Yates
bd3bfe0817
Add warn of default being used
2022-05-02 12:41:24 +02:00
James Fellows Yates
67b074382e
Fix tests
2022-05-02 12:29:00 +02:00
Lucpen
08d5acbeb6
feat added tests for stubs
2022-05-02 11:59:08 +02:00
James Fellows Yates
58e5c6aece
Make variables consistent
2022-05-02 11:55:43 +02:00
James Fellows Yates
6986975bc0
Fix output channels allow BLAST table customisation
2022-05-02 11:39:07 +02:00
Matthias De Smet
bf416f2307
Merge branch 'master' into vardict-java
2022-05-02 10:43:47 +02:00
James Fellows Yates
996385fb0f
Remove MD5sumfor DIAMOND DAA file due to occasioanlly variability
2022-05-02 09:36:34 +02:00
Ramprasad Neethiraj
9a9f3e97de
fix md5sums
2022-05-01 21:51:40 +02:00
James Fellows Yates
44ed38beb8
Merge branch 'diamond-update' of github.com:jfy133/nf-core-modules into diamond-update
2022-04-29 21:06:09 +02:00
James Fellows Yates
39530b5ca7
Bump DIAMOND version to 2.0.15
2022-04-29 21:05:12 +02:00
Carpanzano
41fd2d1557
modifiche
2022-04-29 17:52:12 +02:00
Harshil Patel
4df985a065
Merge branch 'master' into tool/bamtools-split
2022-04-29 16:38:59 +01:00
Carpanzano
6bf0a407f6
modifiche nextflow.config
2022-04-29 15:51:27 +02:00
Simone Carpanzano
d9d0eb393b
Update nextflow.config
2022-04-29 15:39:50 +02:00
Carpanzano
20787514d9
modifiche per il test
2022-04-29 15:11:21 +02:00
James A. Fellows Yates
23c42e9b76
Merge branch 'master' into tool/elprep-merge
2022-04-29 15:11:09 +02:00
Thiseas Christos Lamnidis
4317ad85ae
Passing test
2022-04-29 15:07:32 +02:00
Matthias De Smet
7de207f93f
Merge branch 'master' into diamond-update
2022-04-29 15:02:54 +02:00
Matthias De Smet
bdbf629d93
Merge branch 'master' into tool/bamtools-split
2022-04-29 14:33:28 +02:00
Matthias De Smet
edadc9d216
Merge branch 'master' into tool/elprep-merge
2022-04-29 14:32:12 +02:00
Thiseas Christos Lamnidis
bad832c2ea
Add Sexdeterrmine module
2022-04-29 14:28:45 +02:00
Matthias De Smet
3997d28a77
Merge branch 'master' into subwf/bam_qc
2022-04-29 11:39:18 +02:00
James A. Fellows Yates
983d61763d
Merge branch 'master' into diamond-update
2022-04-29 10:28:38 +02:00
James Fellows Yates
7df2fae746
Clean up test data
2022-04-29 10:26:38 +02:00
James Fellows Yates
42564565b9
Update diamond/blastx diamond/blastp to support all possible output formats
2022-04-29 10:26:17 +02:00
Matthias De Smet
b2e4342105
fix args in nextflow.config
2022-04-29 10:21:22 +02:00
Matthias De Smet
bda132191d
fix args in nextflow.config
2022-04-29 10:13:39 +02:00
CMGG ICT Team
0e01d703ea
remove version md5sum from fixmateinformation
2022-04-29 10:12:52 +02:00
Matthias De Smet
e263f267a7
Merge branch 'master' into bump/picard
2022-04-29 09:48:15 +02:00
Matthias De Smet
ec10f98d55
picard CollectWgsMetrics: update to new cli args ( #1578 )
...
* update to new cli args
* remove bam index from tuple, not needed by program
* bump picard version
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-29 09:32:32 +02:00
Matthias De Smet
b72ec05d69
drop md5sum from versions.yml
2022-04-29 08:19:42 +02:00
Simone Carpanzano
05e283405c
Update test_data.config
2022-04-29 00:13:01 +02:00
Simone Carpanzano
a6026e6d30
Update test_data.config
2022-04-29 00:08:27 +02:00
Simone Carpanzano
a76be27d9f
Update test_data.config
2022-04-29 00:06:55 +02:00