Veit Schwämmle
74a1c1400e
Merge branch 'master' into maxquant
2022-05-16 13:26:35 +02:00
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
ba14355891
revert markduplciatespark changes
2022-05-16 09:54:40 +02:00
FriederikeHanssen
8b4d021189
Merge branch 'master' into gatk_426
2022-05-16 09:50:13 +02:00
Taniguti
ac7fe89a78
Merge branch 'master' into haplocheck
2022-05-13 11:24:10 -03:00
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
6427eeeca0
added tmp-dir + alignment correction
2022-05-13 14:35:22 +02:00
Nicolas Vannieuwkerke
1c2a991429
fixed memory warning
2022-05-13 14:25:53 +02:00
Nicolas Vannieuwkerke
d1f824ae66
updated meta.yml
2022-05-13 14:21:48 +02:00
Praveen
e0dccbb5dd
Changed process label to Medium for GATK4/MarkDuplicates
2022-05-13 13:55:14 +02:00
Nicolas Vannieuwkerke
4f6264f7c3
Merge branch 'new-module-gatk4/splitintervals' of github.com:nvnieuwk/modules into new-module-gatk4/splitintervals
2022-05-13 13:48:35 +02:00
Nicolas Vannieuwkerke
9d53577282
linting
2022-05-13 13:48:33 +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
9f6a1ae4a4
Merge branch 'master' into bowtie2-test-fix
2022-05-13 12:05:48 +01:00
Taniguti
4728b2bcd2
Merge branch 'master' into haplocheck
2022-05-13 07:49:55 -03:00
Lucas Taniguti
86343cb034
feat: add haplocheck
2022-05-13 07:42:09 -03:00
Mahesh Binzer-Panchal
00826dc2e9
Merge branch 'master' into genomescope2
2022-05-13 11:28:47 +02:00
Nicolas Vannieuwkerke
6fa1c8089a
Added memory allocation to VCFeval
2022-05-13 10:03:20 +02:00
FriederikeHanssen
868150e1af
Merge branch 'master' into gatk_426
2022-05-12 19:33:07 +02:00
Rike
5f7b02189a
reverse again, why did tests pass before
2022-05-12 18:35:51 +02:00
Rike
e3a17b699e
update version
2022-05-12 18:19:33 +02:00
Rike
99880654bf
add output default bam
2022-05-12 18:06:15 +02:00
Rike
3fda3903dc
revert markduplciatespark container
2022-05-12 17:40:42 +02:00
Mahesh Binzer-Panchal
308ab8801d
Merge branch 'master' into kat_hist
2022-05-12 16:52:05 +02:00
Rike
f40cfefc08
leftover fixes from refactoring
2022-05-12 16:47:17 +02:00
Rike
fd7ee6799a
update version also for spark containers
2022-05-12 15:55:11 +02:00
Rike
169b2b96c1
update gatk version
2022-05-12 15:45:21 +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
JIANHONG OU
6b960f0e75
fix the typo in motus_profile.
2022-05-12 09:20:32 -04:00
James A. Fellows Yates
3c02e6056c
Merge branch 'master' into antismashlite
2022-05-12 14:53:52 +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
JIANHONG OU
a2dbef3de3
remove the wrong quotes for motus_profile.
2022-05-11 17:49:12 -04:00
Robert A. Petit III
8b6e1aff38
Merge branch 'master' into rp3-add-snippy
2022-05-11 12:28:27 -06:00
JIANHONG OU
aca4b48842
Merge branch 'motus_profile' of github.com:jianhong/modules into motus_profile
2022-05-11 14:23:25 -04:00
JIANHONG OU
ae81311a78
fix the typo when using getExtension for motus_profile.
2022-05-11 14:23:09 -04:00
Matthias De Smet
dcf9c07fc9
Merge branch 'master' into update/bowtie2-align
2022-05-11 19:08:23 +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
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
Matthias De Smet
c8d3de2ad9
restore samtools cmd to defaults
2022-05-11 16:17:30 +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
Matthias De Smet
bcd7fe55b1
Update modules/bowtie2/align/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-05-11 13:59:03 +02:00
Matthias De Smet
9097abf277
Update modules/bowtie2/align/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-05-11 13:58:58 +02:00
Matthias De Smet
971a889e2a
Update modules/bowtie2/align/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-05-11 13:57:27 +02:00
Matthias De Smet
b456d8fa0a
Update modules/bowtie2/align/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-05-11 13:57:19 +02:00
Matthias De Smet
ff4b297827
Update modules/bowtie2/align/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-05-11 13:57:11 +02:00
Matthias De Smet
9dd083fa94
Update modules/bowtie2/align/main.nf
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-05-11 13:55:55 +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
d4f13ebfff
refactor: create new settings input
2022-05-11 12:47:54 +02:00
Moritz E. Beber
5d593bdb45
docs: correct license and input description
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
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
ef2996e4a5
match names in meta and main
2022-05-10 21:47:57 +00:00
Robert A. Petit III
f15848d477
fix typo
2022-05-10 21:44:40 +00:00
Robert A. Petit III
44e13ae439
add module for snippy
2022-05-10 21:31:43 +00:00
Mahesh Binzer-Panchal
cd32c7f744
Merge branch 'master' into kat_hist
2022-05-10 17:03:00 +02:00
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
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
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
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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
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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
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
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
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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
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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
Mahesh Binzer-Panchal
1e55ad987f
Merge branch 'master' into kat_hist
2022-05-06 16:35:51 +02:00
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
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
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
Ramprasad Neethiraj
2990dc8357
callcnv module
2022-05-03 14:20:05 +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
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
012f085378
Prettier
2022-05-03 09:19:39 +00:00
Mahesh Binzer-Panchal
9eff38ff94
Update meta.yml
2022-05-03 09:15:45 +00:00
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
nvnieuwk
8187641280
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:45 +02:00
nvnieuwk
11c6faf433
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:36 +02:00
nvnieuwk
01085b3e09
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:30 +02:00
nvnieuwk
1609dfc96d
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:20 +02:00
nvnieuwk
3cdbdf50fc
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:16:14 +02:00
nvnieuwk
2dff193b54
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:15:59 +02:00
nvnieuwk
7c89af359c
Update modules/vardictjava/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-03 10:15:51 +02:00
Nicolas Vannieuwkerke
49ba3adbde
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-05-03 10:15:33 +02:00
Nicolas Vannieuwkerke
d33253513f
put the version on top of the file
2022-05-03 10:15:30 +02:00
Lauri Mesilaakso
773e6f8e93
Merge branch 'master' into add_compression_to_bam2fq
2022-05-03 11:13:55 +03:00
nvnieuwk
278d41b6bf
Merge branch 'master' into vardict-java
2022-05-03 09:59:05 +02:00
ljmesi
5503903457
Add compression for output fastq file
2022-05-03 09:46:04 +02:00
Ramprasad Neethiraj
6f787aea71
Merge branch 'master' into adding_stub_to_modules
2022-05-03 09:43:16 +02:00
Lauri Mesilaakso
77054795fb
Merge branch 'master' into add_handling_of_alternative_fn_suffix_for_metaphlan3
2022-05-03 09:38:51 +03:00
Nicolas Vannieuwkerke
71c5d21374
ran prettier
2022-05-03 08:34:12 +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
Nicolas Vannieuwkerke
d8782d7976
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-05-03 08:20:13 +02:00
Nicolas Vannieuwkerke
b8a59c2b17
Fixed version annotation
2022-05-03 08:20:10 +02:00
Moritz E. Beber
16aa3915e3
feat: add module for slimfastq
2022-05-02 23:16:59 +02:00
Ramprasad Neethiraj
3194729f82
Merge branch 'master' into adding_stub_to_modules
2022-05-02 18:31:55 +02:00
JIANHONG OU
5735f515f8
fix a typo in version export.
2022-05-02 12:25:48 -04:00
Sateesh Peri
c56b371713
Merge branch 'master' into srst2/srst2
2022-05-02 12:13:11 -04:00
Jasmin F
b8386c42a7
Merge branch 'nf-core:master' into antismashlite
2022-05-02 17:58:19 +02:00
Carpanzano
c07ae8c483
fixed lint in ktimporttaxonomy
2022-05-02 17:47:45 +02:00
Simone Carpanzano
3d9c8a6bb1
Merge branch 'master' into firstbranch
2022-05-02 17:43:33 +02:00
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
Jasmin F
235944f797
Merge branch 'master' into antismash_db_output
2022-05-02 17:11:51 +02:00
Jasmin F
8db0b754c0
Fix commented-out command
2022-05-02 16:56:39 +02:00
jasmezz
6a9f2077cf
Fix unbound variable crash
2022-05-02 16:41:59 +02:00
Lucpen
62c6123ec4
fix gatk4_mutect2 test by changing main.nf
2022-05-02 15:11:57 +02:00
JIANHONG OU
250d64dfde
fix the typo of motus_downloadb.
2022-05-02 08:52:54 -04:00
JIANHONG OU
b14f30936e
Merge branch 'nf-core:master' into motus_downloaddb
2022-05-02 08:42:09 -04:00
JIANHONG OU
31dd31079d
update teh versions.yml
2022-05-02 08:41:41 -04:00
jasmezz
0fc352188b
Fix conda antismash path
2022-05-02 14:40:35 +02:00
JIANHONG OU
0f24e4dcff
add input database and intermediate bam file.
2022-05-02 08:37:12 -04:00
Jasmin F
5cd517e759
Apply suggestions from code review
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-05-02 14:31:40 +02:00
Lucpen
dfabf960dc
Merge branch 'master' into adding_stub_to_modules
2022-05-02 14:20:03 +02:00
ljmesi
ed4dd1a928
Add additional handling of fq.gz file name suffix
2022-05-02 14:16:12 +02:00
Lucpen
f231291e77
fix gatk4_reversam test
2022-05-02 12:58:12 +02:00
James A. Fellows Yates
575258332a
Merge branch 'master' into diamond-update
2022-05-02 12:41:37 +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
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
Praveen
0511e7fbbf
Changed BAI as optional output to handle large genome
2022-05-02 11:35:15 +02:00
Lucpen
8a5bcbc325
fix the stub of gatk4_revertsam
2022-05-02 11:06:08 +02:00
Matthias De Smet
bf416f2307
Merge branch 'master' into vardict-java
2022-05-02 10:43:47 +02:00
Lucpen
6b64f9cb6c
feat added stub to modules
2022-05-02 10:34:14 +02:00
Ramprasad Neethiraj
d2004a2b76
update cnvpytor
2022-05-01 21:14:01 +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
Harshil Patel
4df985a065
Merge branch 'master' into tool/bamtools-split
2022-04-29 16:38:59 +01:00
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
9d0f03d96a
Update modules/elprep/merge/main.nf
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-29 15:07:09 +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
771d5a19f1
fix reference arg
2022-04-29 11:12:24 +02:00
Matthias De Smet
20ebb89ff9
update to long args
2022-04-29 10:52:40 +02:00
James A. Fellows Yates
983d61763d
Merge branch 'master' into diamond-update
2022-04-29 10:28:38 +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
e263f267a7
Merge branch 'master' into bump/picard
2022-04-29 09:48:15 +02:00
Lauri Mesilaakso
1a5a9e7b40
Fix typo ( #1586 )
2022-04-29 09:37:23 +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
00467ac64a
update command line syntax for all tools
2022-04-29 07:57:11 +02:00
Matthias De Smet
6ca6de91f8
bump picard version across the board
2022-04-29 07:47:24 +02:00
Simone Carpanzano
2efa5a09ab
Update main.nf
...
$args line 28
2022-04-29 00:00:13 +02:00
Matthias De Smet
4d913d337d
Merge branch 'master' into tool/bamtools-split
2022-04-28 21:17:46 +02:00
Matthias De Smet
a7ed1477ee
Merge branch 'master' into tool/elprep-merge
2022-04-28 21:14:30 +02:00
Jill V. Hagey, PhD
218769d7df
Update modules/srst2/srst2/main.nf
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Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-04-28 14:41:37 -04:00
Jill V. Hagey, PhD
842ae3982b
Update meta.yml
2022-04-28 14:39:02 -04:00
Jill V. Hagey, PhD
9e7e10305b
Update modules/srst2/srst2/meta.yml
...
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-28 14:02:28 -04:00
Sateesh Peri
f5c4aecde5
Merge branch 'master' into srst2/srst2
2022-04-28 13:49:51 -04:00
Jill V. Hagey, PhD
e29a69077d
add doi
2022-04-28 12:30:04 -04:00
Jill V. Hagey, PhD
5be6afd6b1
changed container
2022-04-28 12:29:39 -04:00
Robert A. Petit III
4b6ee6fc14
Merge branch 'master' into rp3-add-shigatyper
2022-04-28 09:51:36 -06:00
Jasmin F
c740853874
Antismash db output patch 1 ( #3 )
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* Update main.nf
* Update meta.yml
* Update test.yml
2022-04-28 16:42:44 +02:00
Nicolas Vannieuwkerke
4b04ca22dd
Variable name change for var2vcf conversion arguments
2022-04-28 16:38:49 +02:00
Nicolas Vannieuwkerke
d626a1dcd3
Removed a whitespace in meta.yml...
2022-04-28 15:41:43 +02:00
nvnieuwk
a6397fac8f
Merge branch 'master' into vardict-java
2022-04-28 15:34:46 +02:00
Nicolas Vannieuwkerke
bdff37c3d7
Added the statistical tests and conversion to vcf
2022-04-28 15:33:27 +02:00
Nicolas Vannieuwkerke
6678ad4426
Added a header to the VCF
2022-04-28 14:54:20 +02:00
Praveen Raj S
b3e9b88e80
csi output in TABIX ( #1579 )
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* Added: csi output to TABIX
* Added: tests for csi
* Fix tiddit/sv (#1580 )
* Fix fasta ref option for TIDDIT_SV
* Add md5sum's to tiddit/sv tests
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
* Fix: prettier issues
Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com>
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
2022-04-28 14:41:01 +02:00
nvnieuwk
c9404ed266
Merge branch 'master' into vardict-java
2022-04-28 14:30:19 +02:00
Nicolas Vannieuwkerke
40e6e5273d
fix for a linting issue
2022-04-28 14:30:04 +02:00
Nicolas Vannieuwkerke
c6ea41948d
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-04-28 14:29:39 +02:00
Nicolas Vannieuwkerke
bf18604471
fix for a linting issue
2022-04-28 14:29:37 +02:00
JIANHONG OU
cdefbec669
add kimporttext module ( #1560 )
...
* add kimporttext module
* fix the Prettier error.
* fix the Prettier error.
* fix the test.yml
* fix the test.yml
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/krona/ktimporttext/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* update the test files;
simplify the main script of krona/ktimporttext.
* update the test file url for krona ktimporttext
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-28 08:16:26 -04:00
JIANHONG OU
24fb7c89aa
Update modules/motus/downloaddb/main.nf
...
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-04-28 08:14:30 -04:00
Matthias De Smet
c7806e7bef
Merge branch 'master' into vardict-java
2022-04-28 14:12:07 +02:00
JIANHONG OU
61799e80ab
Merge branch 'nf-core:master' into motus_profile
2022-04-28 08:09:47 -04:00
Nicolas Vannieuwkerke
8c98a78d2a
Fixed the issue with the BED file
2022-04-28 14:07:55 +02:00
Daniel Cooke
57cb730e78
Fix tiddit/sv ( #1580 )
...
* Fix fasta ref option for TIDDIT_SV
* Add md5sum's to tiddit/sv tests
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
2022-04-28 14:06:38 +02:00
Praveen Raj S
68f1c27169
Changed tbi as optional output in GATK4 HaplotypeCaller ( #1576 )
...
* Changed tbi as optional output. HC cannot index a VCF from large chromosomes.
* Apply suggestions from code review
* Update modules/gatk4/haplotypecaller/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-04-28 13:41:20 +02:00
Nicolas Vannieuwkerke
45b4a61a15
Some small updates
2022-04-28 13:31:37 +02:00
Nicolas Vannieuwkerke
9df830f79d
Added the .bai and .fai files
2022-04-28 10:23:07 +02:00
Matthias De Smet
484c8f5dfa
Update meta.yml
2022-04-28 09:29:27 +02:00
Matthias De Smet
def580ddb7
Add gzip for compressed output
2022-04-28 09:28:57 +02:00
Nicolas Vannieuwkerke
db43095b1a
Split the bed file into a seperate input
2022-04-28 09:18:15 +02:00
nvnieuwk
1fd4719e9d
Merge branch 'master' into vardict-java
2022-04-28 09:09:07 +02:00
Nicolas Vannieuwkerke
fc942e062a
Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java
2022-04-28 09:08:03 +02:00
Nicolas Vannieuwkerke
85c49a971f
Fixed an issue with wrong file order
2022-04-28 09:07:52 +02:00
Jill V. Hagey, PhD
ecd31fd3cd
remove whitespaces and prettier fix
2022-04-27 19:55:42 -04:00
Jill V. Hagey, PhD
5b6d4fdace
Merge branch 'nf-core:master' into srst2/srst2
2022-04-27 18:19:18 -04:00
jvhagey
839ee59ca1
adding srst2 module
2022-04-27 18:01:28 -04:00
Simone Carpanzano
a5e7943f2b
update krona module
...
add "$args" to the module
2022-04-27 22:43:31 +02:00
Harshil Patel
1b5d3f5ac2
Bump STAR version to 2.7.10a for RSEM modules ( #1573 )
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* Bump STAR version to 2.7.10a for RSEM modules
* Fix tests
2022-04-27 19:21:26 +01:00
Robert A. Petit III
30bd93602f
Merge branch 'master' into rp3-add-shigatyper
2022-04-27 11:37:13 -06:00
Harshil Patel
2134031879
Bump SAMtools version for custom/getchromsizes ( #1572 )
2022-04-27 19:15:11 +02:00
Maxime U. Garcia
10ca39a86f
add intervals possibilities to splitncigarreads ( #1571 )
2022-04-27 16:03:44 +02:00
Matthias De Smet
d9b2c6af1a
Merge branch 'master' into vardict-java
2022-04-27 14:04:05 +02:00
Nicolas Vannieuwkerke
7956d38e61
Fixed the test on nextflow level
2022-04-27 13:18:46 +02:00
Jasmin F
61e740f79c
Add antismash download DB: missing container folders as output channels ( #1567 )
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* Add missing container folders as output channels
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tool name
* Update test output checksum
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-27 12:40:04 +02:00
Matthias De Smet
d57664b576
cleanup TODO's
2022-04-27 11:18:58 +02:00
nvnieuwk
dc62de1a78
Merge branch 'master' into vardict-java
2022-04-27 11:17:33 +02:00
Nicolas Vannieuwkerke
024c992ca7
created the module
2022-04-27 11:12:58 +02:00
Jasmin F
259f993df7
Update tool name
2022-04-27 10:06:58 +02:00
Harshil Patel
85ec13ff1f
Add Trimgalore output for unpaired reads ( #1568 )
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* Add Trimgalore output for unpaired reads
* Use glob instead of outprefix
2022-04-26 19:15:24 +01:00
Sofia Stamouli
1f77bc130b
Update minimap2/align module ( #1537 )
2022-04-26 16:32:20 +02:00
jasmezz
1acde9a7a1
Fix container volume mounts
2022-04-26 16:28:39 +02:00
Jose Espinosa-Carrasco
6a46e7cf11
Allow to pass arguments to the phantompeakqualtools script itself ( #1562 )
...
* Allow to pass arguments to the script itself
* Place args2 correctly
* Define args2 aaaaarrrrgggg
* Testing locally before commiting is a good practice
* Update modules/phantompeakqualtools/main.nf
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-25 19:07:43 +02:00
Maxime U. Garcia
569e07f0af
add samtools/bamtocram modules ( #1561 )
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* add new samtools/bamtocram module
* fix md5sum
* remove md5sum
* Update modules/samtools/bamtocram/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-25 14:32:49 +02:00
Jasmin F
6467e23809
Merge branch 'nf-core:master' into antismashlite
2022-04-25 14:21:54 +02:00
JIANHONG OU
98d318c0e0
init
2022-04-24 07:55:17 -04:00
Matthias De Smet
978f665c0a
Merge branch 'master' into tool/elprep-merge
2022-04-24 10:08:29 +02:00
Sateesh Peri
378fa5fbb4
new module: GAMMA ( #1532 )
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* initial version of gamma module
* remove trailing whitespace
* prettier fix
* hardcode version number
* Update modules/gamma/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/gamma/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/gamma/meta.yml
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
* update meta and prettier
* add whitespaces
* add fasta output and tests
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-23 10:12:06 -04:00
Matthias De Smet
c3f13fdaf6
Merge branch 'master' into tool/bamtools-split
2022-04-22 19:36:18 +02:00
Matthias De Smet
da56a2d509
Update modules/bamtools/split/main.nf
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:36:08 +02:00
Matthias De Smet
2d32267fcd
Update modules/bamtools/split/main.nf
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:36:01 +02:00
Matthias De Smet
7bcede7474
Update modules/bamtools/split/meta.yml
...
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:14 +02:00
Matthias De Smet
2a2ac290c3
Update modules/bamtools/split/meta.yml
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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-04-22 19:34:00 +02:00
Robert A. Petit III
a83202e710
Merge branch 'master' into rp3-add-shigatyper
2022-04-22 08:49:50 -06:00
Robert A. Petit III
c2d2399107
Update modules/shigatyper/main.nf
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Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-22 08:49:44 -06:00
jasmezz
1c1e813c67
Initial module creation
2022-04-22 16:47:48 +02:00
Jose Espinosa-Carrasco
b3e56c83c6
Remove task.cpus from the command ( #1559 )
2022-04-22 15:29:49 +01:00
Harshil Patel
6d88f2da8c
Rename process from STRINGTIE to STRINGTIE_STRINGTIE ( #1546 )
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* Rename process from STRINGTIE to STRINGTIE_STRINGTIE
* Bump Stringtie version to 2.2.1 and remove empty files in tests
* Fix tests for stringtie/merge
Co-authored-by: Júlia Mir Pedrol <mirp.julia@gmail.com>
2022-04-22 15:13:06 +01:00
Harshil Patel
9aadd9a6d3
Replace vanilla Linux Biocontainer with Ubuntu ( #1557 )
2022-04-22 14:50:07 +01:00
CMGG ICT Team
b4af3f1475
test fixes
2022-04-22 15:02:41 +02:00
Sateesh Peri
8f2561c07f
Merge branch 'master' into rp3-add-shigatyper
2022-04-22 09:01:36 -04:00
Matthias De Smet
7e883da904
Revert "make use of dependent on input array size"
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This reverts commit 413980e93a
2022-04-22 14:50:50 +02:00
Matthias De Smet
413980e93a
make use of dependent on input array size
2022-04-22 14:33:16 +02:00
Matthias De Smet
a6e7ecb3a3
Merge branch 'master' into tool/bamtools-split
2022-04-22 13:07:16 +02:00
Matthias De Smet
d57024ddc0
Merge branch 'master' into tool/elprep-merge
2022-04-22 13:05:30 +02:00
Matthias De Smet
c17d1a7a7b
fix output glob ( #1552 )
2022-04-22 13:04:41 +02:00
Matthias De Smet
d9348f3714
Merge branch 'master' into tool/bamtools-split
2022-04-22 13:04:16 +02:00
Matthias De Smet
b1749445d7
fix output glob ( #1551 )
2022-04-22 12:50:17 +02:00
Matthias De Smet
fefffb9bb0
fix output glob
2022-04-22 12:36:32 +02:00
Matthias De Smet
20728acde6
Merge branch 'master' into tool/bamtools-split
2022-04-22 11:57:22 +02:00
Matthias De Smet
2f6382168c
update meta.yml
2022-04-22 11:51:54 +02:00
Matthias De Smet
c4072f274c
fix formatting, fix code style
2022-04-22 11:39:22 +02:00
Matthias De Smet
b4d2e374a0
Merge branch 'master' into tool/elprep-merge
2022-04-22 11:35:48 +02:00
Sofia Stamouli
538dbac98b
Kaiju2table module ( #1545 )
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* Add kaiju2table module
2022-04-22 11:26:30 +02:00
Matthias De Smet
4af5be8de3
Merge branch 'master' into tool/elprep-merge
2022-04-22 11:10:23 +02:00
Matthias De Smet
9e3daae8ef
New module: elprep filter ( #1524 )
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* first commit
* syntax fix
* fix input
* output sam during test for md5sum
* replace md5sum with contains
* add new test data, add extra in/outputs
* cli fixes
* fix outputs
* Update modules/elprep/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/elprep/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/elprep/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix suggestions by @jfy133
* Bit more verbose explanation for bool vals
* define variables
* fix prettier
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 11:08:03 +02:00
Matthias De Smet
a1757897cb
Merge branch 'master' into tool/elprep-merge
2022-04-22 10:20:59 +02:00
Matthias De Smet
90b203d3e9
Tool/elprep split ( #1533 )
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* tool: elprep split
* fixes for testing
* fix tests
* fix test outputs
* create test-yaml
* fix suggestions by @jfy133
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 10:20:05 +02:00
Matthias De Smet
35231d3949
update picard/collecthsmetrics ( #1542 )
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* update picard/collecthsmetrics
* syntax fixes, bugfixes
* add tests
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-04-22 10:13:57 +02:00
Ramprasad Neethiraj
c7329a3a57
add stubs for stranger ( #1543 )
2022-04-22 10:10:43 +02:00
Lucpen
12afb6b0fa
Update samtools view to add input path(index) ( #1539 )
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* feat added index as input, to allow module to be used for subsampling
* fix test
* feat added index to meta.yml
* Update modules/samtools/view/meta.yml
feat corrected description of idea pattern file in meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-22 10:01:47 +02:00
Robert A. Petit III
0095bc91f7
add module for shigatyper
2022-04-21 18:49:42 +00:00
Matthias De Smet
f4c69bc427
Module/bclconvert ( #1485 )
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* bclconvert: initial commit
* add most of tool
* attempt at adding testing stub
* add dockerfile + instructions
* add container to module
* update readme
* more attempts at making stubs work
* finish stub run
* fix ci issues
* more fixes to stub
* add read version check to stub
* fix some tests
* update readme
* fix version number
* syntax fix
* revert edit to output directory
* Update modules/bclconvert/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/bclconvert/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* update meta.yaml
* update thread usage
* Update modules/bclconvert/main.nf
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
* Escape env variable
* Update modules/bclconvert/Dockerfile
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
* fix comments by @Emiller88
* fix task.cpus
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Mark Whelan <7407040+MrMarkW@users.noreply.github.com>
2022-04-21 15:39:22 +02:00
Francesco L
abe025677c
update to kraken2: breaking change - output channels renamed ( #1525 )
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* updated kraken2 module to include optional classification of each input reads, and make fastq outputs optional
NB: this is a breaking change, because the output channels have been renamed as a consequence of changes
* updated yml
* pigz command made optional, in order to be executed only if fastq of classified/unclassified reads are saved
* updated test yaml file for kraken2
* fixed TODOs and renamed variables and outputs
* untar in conda cannot keep same md5sum of version, and therefore md5sum check removed
* improved description of the options
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-21 14:33:59 +02:00
Jasmin F
d07d270743
Antismashlite download databases ( #1426 )
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* Create module antismashlitedownloaddatabases
* Corrected user-specification of database directory
* Updated test.yml
* Apply suggestions from code review
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix typo in test.yml
* Feed database files via docker/singularity mount)
* Add external db file mounts to the containers
* Fixed docker command in main.nf
* Apply prettier
* Apply prettier and add PWD
* Add more output to test.yml
* Add more output paths to test.yml
* Fixed test.yml
* Apply suggestions from code review
Add documentation of why we need to mount files to the containers.
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Fix code linting errors (remove trailing whitespaces)
* Fix code linting error (remove trailing whitespace)
* Fix errors from Prettier linting
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-21 10:38:17 +02:00
Maxime U. Garcia
37bf3936f3
add decompress possibilities to bgzip ( #1540 )
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* add decompress possibilities to bgzip
* spacing
2022-04-20 16:26:56 +02:00
louperelo
6c45773c0b
add module AMPlify ( #1498 )
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* add module AMPlify
* Apply suggestions from code review
Thanks for the review!
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* removed trailing whitespaces
* Apply suggestions from code review
Thanks again!
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
* Apply suggestions from code review
Thank you for the suggestions!
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Apply suggestions from code review
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* including review suggestions
* fix versions.yml
* add model_dir input
* add model_dir to meta.yml
* complete faa pattern in meta.yml
* add fa.gz to pattern
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-20 11:53:26 +02:00
Maxime U. Garcia
705f8c9ac4
Add samtools/collatefastq module ( #1536 )
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* add samtools/collatefastq module
* update yml file
* improve output
2022-04-20 10:05:17 +02:00
Matthias De Smet
bddb88dfaf
Merge branch 'master' into tool/bamtools-split
2022-04-19 15:33:49 +02:00
Matthias De Smet
07982d6cb1
fix command line, fix meta.yml
2022-04-19 15:31:39 +02:00
Matthias De Smet
b35264e919
bugfixes
2022-04-19 15:11:37 +02:00
Matthias De Smet
6723ca7f90
bump version, add merge before split
2022-04-19 15:05:02 +02:00
Matthias De Smet
553c1bcf9d
Merge branch 'master' into tool/elprep-merge
2022-04-19 11:28:04 +02:00
Matthias De Smet
ad15d1b792
update label
2022-04-19 11:27:55 +02:00
Matthias De Smet
ccef7f8579
alignment
2022-04-19 11:26:01 +02:00
Anders Jemt
a6cb75174b
Add variant catalog ch to stranger ( #1508 )
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* Add optional variant catalog input
* fix for no variant catalog test
Co-authored-by: ljmesi <37740329+ljmesi@users.noreply.github.com>
Co-authored-by: Lauri Mesilaakso <john.mesilaakso@gmail.com>
2022-04-19 10:53:39 +02:00
James A. Fellows Yates
87005786e0
Update modules/motus/downloaddb/main.nf
2022-04-17 21:18:55 +02:00
James A. Fellows Yates
ec23ebc7c5
Update modules/motus/downloaddb/main.nf
2022-04-17 21:17:59 +02:00
JIANHONG OU
9a158acb50
Merge branch 'motus_downloaddb' of github.com:jianhong/modules into motus_downloaddb
2022-04-17 11:22:25 -04:00
JIANHONG OU
407d0bb752
update motus_downloaddb
2022-04-17 11:22:23 -04:00
JIANHONG OU
51214d655b
Update modules/motus/downloaddb/main.nf
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:19:58 -04:00
JIANHONG OU
32d5257def
Update modules/motus/downloaddb/meta.yml
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:12:08 -04:00
JIANHONG OU
d247ef4a0d
Update modules/motus/downloaddb/main.nf
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:10:54 -04:00
JIANHONG OU
2551201f43
Update modules/motus/downloaddb/main.nf
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:10:48 -04:00
JIANHONG OU
f1f1df984c
Update modules/motus/downloaddb/main.nf
...
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-17 11:06:06 -04:00
JIANHONG OU
ee04fc2737
add module motus_downloaddb
2022-04-14 12:56:42 -04:00
Matthias Hörtenhuber
c7def8707b
fix incorrect yaml formatting. ( #1264 )
2022-04-14 13:35:01 +02:00
Sofia Stamouli
be4ae28c3c
Add centrifuge_kreport module ( #1514 )
2022-04-13 15:33:51 +02:00
Maxime U. Garcia
e04970b7d2
typo in command line ( #1523 )
2022-04-13 15:15:44 +02:00
Sofia Stamouli
8856f127c5
Update input in kaiju_kaiju module ( #1522 )
2022-04-13 14:53:08 +02:00
Maxime U. Garcia
4f5274c3de
feat: remove read_group which should be set up with task.ext.args ( #1521 )
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* feat: remove reat_group which should be set up with ext.args
* fix: simplify dragmap command
2022-04-13 14:30:34 +02:00
Matthias De Smet
0f7c046477
first commit
2022-04-13 12:51:17 +02:00
Maxime U. Garcia
409af2f27c
Improve syntax/logic coherence in all gatk4 plugins ( #1459 )
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* feat: code polishing
* Apply suggestions from code review
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* code polishing
* more code polishing
* code polishing
* tests for applybqsrspark
* fix typo
* no need to check md5sum for versions.yml
* fix: use correct syntax
* code polishing again
* add tests for markduplicatesspark
* simplify mergevcfs tests
* add tests for baserecalibratorspark
* fix: path to entry
* code polishing
* fix linting
* simplify module
* update meta.yml
* fix pair mode
* fix: MITO mode
* more tests
* fix command
* bad copy paste
* fix typos
* fix tests
* fix test
* update meta.yml
* correct versions.yml in all test.yml
* code polishing
* code polishing
* more code polishing
* fix args
* add tmpdir for all
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-04-12 17:15:39 +02:00
Matthias De Smet
b59713e623
Tool/snap aligner single ( #1510 )
...
* first commit
* add tool
* fix tests
* fix indents
* Update modules/snapaligner/single/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix comments
* fix versions
* prettier
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-12 11:20:35 +02:00
Matthias De Smet
09125979cc
Tool/snap aligner paired ( #1509 )
...
* first commit
* edit main.nf
* edit tests
* run prettier
* fix test
* indent script
* Update modules/snapaligner/paired/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/snapaligner/paired/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix version nr
* update meta
* fix versions
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-12 11:02:10 +02:00
FriederikeHanssen
ffedf09b6e
Revert manta changes ( #1518 )
...
* Fix typo
* Revert to have target bed matched with sample info
* Add comment on design decision
2022-04-12 10:40:06 +02:00
James A. Fellows Yates
2d38566eca
Add MEGAN/RMA2INFO ( #1513 )
...
* fix: remove left-over unnecessary code
* Add megan/rma2info
* Attempt at fixing test
* Right yml formatting
* Get the versios reporting correct
2022-04-12 08:35:36 +02:00
FriederikeHanssen
897c33d5da
Samtools version update ( #1507 )
...
* Fix typo
* update version to 1.15.1
* Fix md5sums
* update mulled containers
* update md5sums
* update md5sums
2022-04-11 14:26:28 +02:00
Michael L Heuer
8dc680d3b3
Update dsh-bio to version 2.0.8. ( #1483 )
2022-04-09 11:13:47 -05:00
Matthias De Smet
d4160c669b
Tool/crosscheckfingerprints ( #1505 )
...
* first commit
* first commit
* update test.yml
* update test.yml
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
* add support for vcf haplotype maps
* update test
* update test data config, use test data
* fix exit code
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/crosscheckfingerprints/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* remove unused stub
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-08 10:02:10 -04:00
Matthias De Smet
e19a9a2474
new tool: staden_io_lib ( #1499 )
...
* new tool: staden_io_lib
* update docker containers
* add test.yml
* add fai index input
* typo
* fix version.yml
* update md5sum
* omit md5sum for cram
* move scramble to submodule
* add missing in/output
* remove some comments
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-04-08 09:54:15 -04:00
Matthias De Smet
f57f085912
new tool snap-aligner/index ( #1506 )
...
* add snapaligner/index
* output fixes
* fix outputs
* fix tests
* update inputs
* fix more bugs
* fix linting
* Update modules/snapaligner/index/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/snapaligner/index/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* fix comments
* fix indents
* fix escaping
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-08 14:41:08 +02:00
FriederikeHanssen
9ae34a01d1
Fix Controlfreec: Add stub runs to test single sample input & make conda work with R scripts ( #1504 )
...
* Fix typo
* Add stub runs for testing input without matched normals
* Add missing -stub-run
* remove empty file checksum tests and change workflow names
* test controlfreec naming
* fix output file names
* fix output file names
* fix output file names
* fix conda and container path difference for R scripts
* update tar version to work with conda
* fix version number in docker
* try to fix path to script, pretty sure it won't work
* try new ways to set path with wildcard
* try which
* add which but with escape
* remove comment
2022-04-08 11:43:40 +02:00
Lucpen
f079367416
Picard liftover vcf ( #1431 )
...
* Building Picard liftovervcf module
* Building Picard liftovervcf module_test
* Building Picard liftovervcf pytest
* Module for picard liftover vcf created
* Fixed files after linting test
* Fixed trailing whitespace
* Checked files with prettier
* further formatting with prettier
* Fixed test.yml
* Fixed input variable names
* Changed contain test.liftef.vcf
* Changed contain in test.yml test.liftef.vcf
* Run prittier
* Going back to previous version of test.yml
* downgrading picard to 2.26.10 from 2.26.11
* Update modules/picard/liftovervcf/main.nf
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/liftovervcf/main.nf
Print available memory
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Output from .vcf to .vcf.gz
* Added spaces to align emit
* Update modules/picard/liftovervcf/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/liftovervcf/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Update modules/picard/liftovervcf/meta.yml
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
* Removing md5sum test
Co-authored-by: jemten <jemten@users.noreply.github.com>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-04-07 07:50:58 -04:00
Sofia Stamouli
d2726fcf75
Update centrifuge/centrifuge ( #1495 )
2022-04-07 11:46:34 +02:00
Matthias De Smet
dc95e67e15
New tool: biobambam/bamsormadup ( #1478 )
...
* add bamsormadup
* fix yaml
* add test.yml
* Update tests/modules/biobambam/bamsormadup/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* test meta.yaml: remove md5sums
* Tool bamsormadup:
- add (optional) reference input
- add bam index ouput
- add cram output option
- make metrics output: more general
* fix input and output formats
* update input file description
* drop sam output, goes against nf-core regs; add input check for cram files
* fix typo
* Update modules/biobambam/bamsormadup/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* improve ref fasta name
* fix if else shorthand
* fix syntax error
* kind of fix tests
* set fixed suffix for metrics file to keep it in line with picard and bammarkduplicates2
* fix command line
* update test.yml
* add support for multiple input bams
* Update modules/biobambam/bamsormadup/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/biobambam/bamsormadup/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/biobambam/bamsormadup/test.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-04-06 08:18:23 +02:00
Matthias De Smet
797ce3254e
Update: biobambam/bammarkduplicates2 to v2.0.183 ( #1493 )
...
* bump version, remove md5sums from test
* re-add md5sums
2022-04-05 11:06:46 +02:00
Moritz E. Beber
879d42c5e2
Refactor adapterremoval ( #1491 )
...
* refactor: insert .fastq file extensions
* style: insert whitespace
* refactor: create paired output
* refactor: rename settings from log
Requested by @jfy133
* tests: correct expected output
* fix: remove settings option due to default
* chore: rename output patterns
* refactor: omit paired files in single-end
* refactor: rename output to settings
2022-04-04 21:40:35 +02:00
James A. Fellows Yates
ae48653bd2
DASTool output channels update ( #1489 )
...
* fix: remove left-over unnecessary code
* Make summary output optional as not generated if no sufficiently HQ bins found
* Make contig2bin optional as only generated if sufficient HQ bins found
2022-04-04 13:31:36 +02:00
Ramprasad Neethiraj
cb54d1ebd7
update stubs ( #1488 )
2022-04-04 13:18:02 +02:00
Sofia Stamouli
6a11c5a222
Fix untar for centrifuge ( #1472 )
2022-04-04 10:18:11 +02:00
James A. Fellows Yates
f1c5384c31
Add PRINSEQPLUSPLUS ( #1481 )
...
* fix: remove left-over unnecessary code
* Add prinseq++
* Remove last todo
* Fix tests due to variability of output FASTQs (reads can be ordered differently between runs)
* Apply suggestions from code review
2022-04-03 16:06:22 +02:00
Ramprasad Neethiraj
67c1bc9568
Add stubs to cnvpytor module ( #1473 )
...
* callcnvs stub and tests
* partition stub and test
* histogram stub and test
* importreaddepth stub and tests
* update module scripts
Co-authored-by: Sima Rahimi <sima.rahimi@gu.se>
2022-04-01 17:35:15 +02:00
James A. Fellows Yates
8ce6810787
Update DASTool to 1.1.4 ( #1471 )
...
* fix: remove left-over unnecessary code
* Update DASTool
* Fix tests
* Fix test.ymls
* Fix container build version
* Make tests less strict to account for variability
* Apply suggestions from code review
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Add missing description
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-04-01 11:33:07 +02:00
Jose Espinosa-Carrasco
5e7daa7b96
Add task.ext.args to phantompeakqualtools and finish the module ( #1474 )
...
* Add --max--ppsize option
* Add args to phantompeakqualtools and all the missing files (test, yml, ...)
* Fix tests
* Add the nextflow.config
* Fix tests
2022-03-31 22:59:21 +01:00
Maxime Borry
64b06baa06
Update PyDamage module ( #1467 )
...
* add pydamage module
* remove TODOs
* split module by subcommands
* update version parsing
* remove forgotten TODOs
* update module names
* remove old holistic module
* Update modules/pydamage/analyze/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add keywords
* update resource requirement
* Update modules/pydamage/filter/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/pydamage/filter/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* merge from upstream
* update pydamage from upstream
* add freebayes
* update pydamage test from upstream
* fix meta.yml
* update functions.nf
* update test.yml
* update version parsing
* update version parsing
* fix indentation
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs
* Update modules/freebayes/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add bed test
* add metabat2 module
* only freebayes
* remove metabat2
* update md5sum because of vcf including date of the day
* add keyword
* rescue conflicted files
* attempt to fix ECLint
* add pytest workflow for metabat
* remove -
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* add optional inputs/outpus
* remove trailing whitespace
* compressing and removing not reproducible md5sums
* follow symlinks while decompressing
* Update tests/modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update tests/modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* split tests
* export env variable
* Update modules/metabat2/jgisummarizebamcontigdepths/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/metabat2/metabat2/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* answer PR comments and switch to bgzip
* add bacillus fragilis alignments
* add meta to samtools/faidx
* move to bgzip
* update freebayes test results
* bump pydamage version to 0.70
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-31 09:18:18 -04:00
Sébastien Guizard
794f84534b
New Module: gstama/polyacleanup ( #1468 )
...
* 📦 NEW: Add gstama/polyacleanup
polyacleanup script remove remaining polyA tails from FLNC reads (Pacbio isoseq3)
* 🐛 FIX: Prettier: replace simple quote by double quote
* 🐛 FIX: Update TEMPLATE to nf-core 2.4
* 👌 IMPROVE: Compress outputs
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
2022-03-31 09:11:51 -04:00
Ramprasad Neethiraj
eeda4136c0
Update cat module ( #1469 )
...
* fix cat stub
* add test
* commit suggestions
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-03-31 13:42:44 +02:00
Ramprasad Neethiraj
233f2e728b
fix cnvpytor links ( #1470 )
2022-03-31 10:53:26 +02:00
Moritz E. Beber
0de6406217
feat: add module for seqkit stats ( #1466 )
2022-03-30 23:01:17 +02:00
Ramprasad Neethiraj
fd5f6f5f4f
Revert recent changes made to some of the modules ( #1463 )
...
* revert changes to modules
* fix tests
* fix kraken2
* fix untar
* fix cat
* add blank lines
* fix typo
2022-03-30 20:21:06 +02:00
Ramprasad Neethiraj
a973b68200
svdb update to 2.6.0 ( #1465 )
2022-03-30 14:50:27 +02:00
FriederikeHanssen
1ec1868264
Fix typo ( #1464 )
2022-03-29 13:13:41 -04:00
Jose Espinosa-Carrasco
dbb46c9b63
Bump chromap version 0.2.1 ( #1462 )
2022-03-29 16:44:19 +02:00
Ramprasad Neethiraj
49b18b1639
add stub to modules used in raredisease pipeline ( #1206 )
...
* add stub section
* add stub for bcftools norm
* add stub to more modules
* fix expansionhunter tests
* revert changes -picard
* Update stub to write version no.s to a file
* add picard
* revert picard again
* add stubs to more modules
* fix bwamem2
* add bcftools view
* add stubs
* fix svdb query
* review suggestions
2022-03-28 17:48:39 +02:00
James A. Fellows Yates
240ee4328c
Dastool update to allow non-gzipped inputs ( #1458 )
...
* fix: remove left-over unnecessary code
* Make gzipping optional for DAS_Tool scaffolds2bin
* Add optional unzipping
* Make gunzip optional for DAS_Tool scaffolds2bin
* Apply suggestions from code review
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
* Update modules/dastool/scaffolds2bin/meta.yml
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-03-28 16:29:46 +02:00
Tanja Normark
1f483d9203
Add kaiju_kaiju module ( #1448 )
...
* Added kaiju_kaiju module
* Update modules/kaiju/kaiju/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/kaiju/kaiju/main.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update modules/kaiju/kaiju/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update keywords
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Update output file naming
* Update output file naming
* update spacing for lint
* Update input file patterns
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-03-28 14:28:50 +02:00
Ramprasad Neethiraj
cc671a5f3c
Update svdb/merge ( #1449 )
...
* fix error
* fix input string
2022-03-27 14:15:43 +02:00
Edmund Miller
5832fbc225
Fix homer/maketagdirectory output collision ( #1456 )
...
* fix(homer): Update tagdir to have a prefix
Otherwise they have a naming collision
* test(homer): Update paths
* style(homer): Align ,'s
* chore(homer): Update md5sums
2022-03-27 03:17:42 +00:00
FriederikeHanssen
5acf301ddd
add freec2circos script ( #1454 )
...
* add freec2circos script
* remove todo statements
2022-03-26 21:25:29 +01:00
FriederikeHanssen
28e5211b35
add makegraph script ( #1452 )
...
* add makegraph script
* allow renaming of output files
* allow renaming of output files
2022-03-25 20:49:08 +01:00
FriederikeHanssen
8a64e73af2
add freec2bed script ( #1453 )
2022-03-25 20:31:52 +01:00
FriederikeHanssen
4efa8da5c5
controlfreec significance ( #1451 )
...
* controlfreec significance
* move freec files to own subfolder
* Fix meta.yml naming
* Fix meta.yml naming
* Fix linting
* Forgot to refactor
* forgot more refactoring
* Too much refactoring on output paths
* Too little refactoring here
* update checksum
2022-03-25 18:22:17 +01:00
Edmund Miller
27936729f2
Add samtools to homer/maketagdirectory to use bam files ( #1437 )
...
* fix(homer): Update dependancies for maketagdirectory
Closes #1363
* test(homer): Add tests for bam usage
* style(homer): Rename meta test
* fix(homer): Update args order and add missing \\
* docs(homer): Add DESeq2 and edgeR
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* test(homer): Update md5sum
* test(homer): bam => sam
* fix(homer): Use nextflow conda recipe instead of biocontainers with commas
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-03-25 17:13:30 +00:00
Edmund Miller
7111e571cc
Split preseq lcextrap and ccurve ( #1440 )
...
* fix(preseq): Update lcextrap file name
* chore(preseq): Bump lcextrap image
* feat: Initialize preseq c_curve
* docs(preseq): Update documentation
2022-03-25 17:11:40 +00:00
Edmund Miller
1fb1801dcb
refactor(homer): Update output path for bedGraph ( #1438 )
...
This allow for caching because otherwise it modifies the tag directory input
2022-03-25 13:54:09 +00:00
Edmund Miller
98ed71c8f6
feat(homer): Add pos2bed module ( #1435 )
...
* feat(homer): Add pos2bed module
* test(homer): Pass bed format
* test(homer): Add upstream dependencies to avoid regressions
* Update modules/homer/pos2bed/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-03-25 13:29:36 +00:00
FriederikeHanssen
3d31fa4d04
CAT: Use meta map and supply output file name via modules.config ( #1446 )
...
* Use meta map and supply output file name via modules.config
* Remove all def declarations to make it work
* update tests & remove extra .
* fix ze tests
* update meta.yml with meta map info
* add tag line now that meta is available
2022-03-25 14:01:57 +01:00
Maxime U. Garcia
e786457fb0
feat: add readgroup info + reorder samtools command line to mimic bwamem ( #1447 )
2022-03-25 11:26:47 +01:00
FriederikeHanssen
b5825fe6b3
Mpileup also likes intervals ( #1445 )
...
* Mpileup also likes intervals
* Also update meta yml with inclusive input and intervals
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-03-25 07:46:51 +01:00
Edmund Miller
e3a5795652
Homer/findpeaks improvements ( #1436 )
...
* fix(homer): Update expected file path to improve caching
* docs(homer): Update findpeaks
* test(homer): Add maketagdirectory dependency
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-25 02:44:12 +00:00
Robert A. Petit III
d16f1ea4d7
add module for panaroo, fix pirate tests ( #1444 )
...
* add module for panaroo
* update pirate test yaml
* update panaroo test yaml
* update pirate test yaml md5s
* Update main.nf
* Update main.nf
* pin bioperl version
2022-03-24 20:11:04 -06:00
Edmund Miller
6806cd1de9
feat(bbmap): Initialize pileup module ( #1441 )
...
* feat(bbmap): Initialize pileup module
* test(bbmap): Update outputs
* test(bbmap): Add pileup tags
* style(bbmap): Add in when
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-03-24 17:38:24 -06:00
Edmund Miller
fe088745e0
style(deeptools): Indent script ( #1439 )
2022-03-24 19:44:31 +00:00
Robert A. Petit III
608bb22598
Update dragonflye to latest version ( #1442 )
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* Update dragonflye to latest version
* trigger ci
2022-03-24 14:56:32 -04:00
Robert A. Petit III
dfbb0bc17c
update bakta to latest version (v1.4.0) ( #1428 )
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* update bakta to latest version (v1.4.0)
* Update test.yml
* remove empty file md5sums
* bakta was rebuilt to fix dependencies on bioconda
* trigger ci
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
2022-03-24 10:49:17 -06:00
Annick Renevey
1dddf1ce94
update star/align to include an optional sam output (support for --chimOutType SeparateSAMold option) ( #1378 )
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Co-authored-by: Praveen Raj S <43108054+praveenraj2018@users.noreply.github.com>
2022-03-23 13:13:58 +01:00
Moritz E. Beber
9c386c5dd8
Add bracken ( #1423 )
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* feat: add template for Bracken
* chore: update version
* refactor: change command build
* refactor: rename report variable, change quotes
* docs: remove refactored input parameter
* fix: correctly assign arguments to options
* tests: set up single and paired end tests
* style: apply prettier
* chore: change data sources to official ones
* refactor: rename test workflows
* tests: use correct input to the new UNTAR module
* chore: update md5sums
2022-03-22 16:40:21 +01:00
James A. Fellows Yates
e080f4c8ac
Untar unzip meta ( #1408 )
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* fix: remove left-over unnecessary code
* Adds support for meta lists for unzip and untar
* Fix test inputs
* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple
* Update all modules to support extraction of decompressed file from untar/unzip new meta + file tuple
* Fix MALTEXTRACT/AMPS
* Fix further modules
* Fix cellranger
* Apply suggestions from code review
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-03-21 14:49:28 +01:00
James A. Fellows Yates
8c00897853
Add AdapterRemovalFixPrefix ( #1424 )
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* Add AdapterRemovalFixPrefix
* Prettifying
Co-authored-by: Alexander Peltzer <apeltzer@users.noreply.github.com>
2022-03-21 11:26:12 +01:00
Ramprasad Neethiraj
5297d27fbf
update svdb to version 2.5.2 ( #1390 )
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* update svdb version and tests
* update link
2022-03-21 10:39:34 +01:00
Harshil Patel
f425aa3cea
Add outputs for umitools dedup summary stats ( #1422 )
2022-03-18 20:21:41 +00:00
James A. Fellows Yates
15c7190e22
Deeparg singularity container fix 2 ( #1406 )
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* fix: remove left-over unnecessary code
* Switch to more portable solution for singularity container issue by using bind paths
* Fix input collision of dummy files
* Repalce dummy with which bash
* Remove dummy usage from tests
* Apply suggestions from code review
* Fix singularity typo
2022-03-18 16:21:55 +01:00
Sofia Stamouli
ea41a8a6f7
Add centrifuge module ( #1410 )
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* Add centrifuge module
* Add centrifuge module
* Add centrifuge module
* Add centrifuge module
2022-03-18 15:39:27 +01:00
Edmund Miller
f080015754
Prettier ( #1405 )
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* style: Add prettier config files
* build: Add prettier vscode extension
* ci: Replace markdownlint and yamllint with prettier
* style: Run prettier
* style: Use indent of 2 for markdown as well
https://github.com/nf-core/tools/pull/1470#issuecomment-1071028358
* style: Fix indent
* style: Let editorconfig take over tab widths
* style: yaml => yml
* ci: Run prettier once
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
Co-authored-by: Phil Ewels <phil.ewels@scilifelab.se>
2022-03-18 14:27:50 +01:00
