Adam Talbot
f19ec865aa
vcf2maf module with built in VEP ( #1768 )
...
vcf2maf module created
Additions:
- vcf2maf module created
- If VEP is present in PATH, it is added to command
- If VEP is missing, it is ignored (recommended to skip with --inhibit-vep)
- VEP version automatically added to versions.yml
- Uses VEP cache during testing which is added to test-datasets in https://github.com/nf-core/test-datasets/pull/563
- Default Docker image includes VEP and vcf2maf
- Test includes without VEP.
Relates to #490
2022-06-20 18:27:12 +02:00
nvnieuwk
6e7c0e945b
new module vcf2db ( #1795 )
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* added vcf2db
* fix test.yml
* possible fix for failing tests
* fix version number
* fix test.yml
* removed some comments
2022-06-17 15:54:02 +02:00
alyssa-ab
c1eb9cce44
Trimmomatic ( #1757 )
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* Trimmomatic main only first draft
* Add test files
* SE PE Adjustment
* Remove extra reads input
* chore: Remove TODOs
* Apply suggestions from code review
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
* fix(trimmomatic): Handle SE output correctly
Since there's never going to be unpaired reads for SE reads we can get
away with it for SE
* fix(trimmomatic): Use correct elvis operator to handle logic
* fix(trimmomatic): Add hack to work with SE and PE reads
* Update test.yml
* use the PE and SE trimming correctly
* Made user set adaptors
* Add documentation
* test(trimmomatic): Add files to pytest_modules
* test(trimmomatic): Update name of failing test
Co-authored-by: Edmund Miller <edmund.a.miller@protonmail.com>
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
2022-06-17 13:18:15 +00:00
Matthias De Smet
f32dc15414
update bclconvert module, as used in nf-core/demultiplex ( #1569 )
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* update bclconvert module, as used in nf-core/demultiplex
* reconfigure test with new test data
* update test
* formatting
* update outputs, update meta
* update module and test
* update test config, test.yml
* fix linting
* emit logs and reports as dir
* fix typo, recreate test.yml
* fix linting
Co-authored-by: CMGG ICT Team <ict@cmgg.be>
2022-06-16 15:03:13 +02:00
Robert A. Petit III
052b9f2fe9
add module for plasmidfinder ( #1773 )
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* add module for plasmidfinder
* Update test.yml
2022-06-15 10:25:51 -06:00
Robert A. Petit III
1fe4cb942f
add module for ariba ( #1731 )
2022-06-15 10:18:31 -06:00
Mahesh Binzer-Panchal
0af6adef55
Add MerquryFK PloidyPlot ( #1780 )
2022-06-14 20:50:58 +02:00
Mahesh Binzer-Panchal
e91e99db30
Add GeneScopeFK ( #1781 )
2022-06-14 20:49:06 +02:00
Mahesh Binzer-Panchal
8ded6d441a
Add MerquryFK ( #1778 )
...
* Add MerquryFK
* Change resource allocation
2022-06-14 16:36:02 +02:00
Mahesh Binzer-Panchal
fd5aea0b76
Add FastK/Histex ( #1776 )
2022-06-14 16:30:37 +02:00
nvnieuwk
1a4ab76618
new module rtgtools/pedfilter ( #1777 )
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* new module rtgtools/pedfilter
* removed checksum due to the presence of a date in the file
2022-06-14 16:02:18 +02:00
Mahesh Binzer-Panchal
4e308c131e
FastK/fastK ( #1739 )
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* Add FastK/FastK
* Add ktab and prof outputs
* Add the hidden files necessary for the optional files
* Update image
* Apply suggestions from code review
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
2022-06-14 13:39:52 +02:00
8b2a473f58
New module: krakentools/kreport2krona ( #1746 )
...
* Add module definition for kreport2krona
* Add metadata for kreport2krona module
* Add tests for kreport2krona
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-06-13 20:14:44 +02:00
Merlin Szymanski
8f199c4fa4
Create atlas/splitmerge Module ( #1756 )
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* Add atlas/splitmerge module
* Finish the tests for atlas/splitmerge
* Prettier
* Update modules/atlas/splitmerge/meta.yml
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
* Remove curly brackets from meta.yml parameters
For single-file outputs, as reviewed
* Lintung: Remove trailing white-space
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-06-13 15:09:32 +02:00
Robert A. Petit III
81232af296
add module for mcroni ( #1750 )
...
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
2022-06-13 15:04:01 +02:00
FriederikeHanssen
5b27af025a
Merge branch 'master' into manta_convert
2022-06-13 09:29:50 +02:00
Rike
650076cacf
add manta conversion script
2022-06-11 13:01:18 +02:00
Taniguti
547f483b74
Merge branch 'master' into haplocheck
2022-06-10 20:39:33 -03:00
Jasmin F
7027719c67
Merge branch 'master' into r-ampir
2022-06-10 14:57:24 +02:00
Thiseas C. Lamnidis
9948e9fe21
Merge branch 'master' into sexdeterrmine
2022-06-10 11:03:18 +02:00
James A. Fellows Yates
c9db677a45
Merge branch 'master' into r-ampir
2022-06-09 19:28:37 +02:00
Nicolas Vannieuwkerke
fe9e4ece00
new module gatk4/reblockgvcf
2022-06-09 14:56:55 +02:00
James A. Fellows Yates
1fc0d3de4b
Merge branch 'gatk3-indelrealigner' into upstream-for-indel
2022-06-08 20:30:19 +02:00
James A. Fellows Yates
4a2157e5ab
Merge branch 'master' into gatk-realigntargetcreator
2022-06-08 20:15:02 +02:00
Taniguti
89bffe3a5e
Merge branch 'master' into haplocheck
2022-06-08 15:00:06 -03:00
Lucas Taniguti
f26979c44e
tests: add input to test_data.config
2022-06-08 08:10:25 -03:00
Ramprasad Neethiraj
16e5e6093c
Merge branch 'master' of https://github.com/nf-core/modules into rhocall
2022-06-07 14:45:09 +02:00
Taniguti
a2e2d50494
Merge branch 'master' into haplocheck
2022-06-07 08:16:22 -03:00
Ramprasad Neethiraj
9d6697bdea
template
2022-06-07 12:14:40 +02:00
James A. Fellows Yates
d292f822e4
Merge branch 'master' into gatk-realigntargetcreator
2022-06-03 21:33:22 +02:00
James A. Fellows Yates
d2b240a17a
Merge branch 'master' into gatk-unifiedgenotyper
2022-06-03 21:24:09 +02:00
Robert A. Petit III
24ca2ed464
Merge branch 'master' into rp3-add-snippy
2022-06-03 13:01:05 -06:00
James Fellows Yates
544b62df45
Star work on GATK UG
2022-06-02 21:11:17 +02:00
James A. Fellows Yates
abc619a3e2
Merge branch 'master' into gatk-realigntargetcreator
2022-06-02 20:24:24 +02:00
Nicolas Vannieuwkerke
e53d091a6d
added dragstr model to haplotypecaller
2022-06-02 14:08:09 +02:00
nvnieuwk
a339f9818a
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
2022-06-02 13:42:56 +02:00
nvnieuwk
4b430e8ece
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
2022-06-02 13:41:20 +02:00
Matthias De Smet
f58771c47f
Merge branch 'master' into update/untar
2022-06-02 13:38:53 +02:00
Nicolas Vannieuwkerke
2a45d42868
added the calibratedragstrmodel module
2022-06-02 13:17:06 +02:00
Matthias De Smet
51be617b1c
fix untar output dir
2022-06-02 11:09:55 +02:00
SusiJo
9fc9be3e7b
Merge remote-tracking branch 'origin/master' into cnvkit_bam
2022-06-01 17:35:47 +02:00
SusiJo
f6953b5147
adjust cnvkit/batch for germline mode
2022-06-01 17:35:02 +02:00
James A. Fellows Yates
5a94794793
Merge branch 'master' into r-ampir
2022-06-01 09:18:54 +02:00
James Fellows Yates
c1ac3fbb59
Skeleton
2022-05-31 20:13:48 +02:00
Nicolas Vannieuwkerke
80366924fd
added gatk4/composestrtablefile
2022-05-31 16:08:13 +02:00
James Fellows Yates
7ffe98ac8b
Add gatk/indelrealigner
2022-05-30 21:12:21 +02:00
jtangrot
1c99ffd876
Add vserach usearch_global
2022-05-30 08:50:27 +02:00
Sateesh Peri
ead3679829
Merge branch 'master' into rp3-add-snippy
2022-05-26 03:04:19 -04:00
jasmezz
77b5986463
Create ampir module
2022-05-25 13:27:10 +02:00
Jill V. Hagey, PhD
b1dd1d8a52
Merge branch 'nf-core:master' into gamma-update
2022-05-24 19:28:06 -04:00
jvhagey
bb999395aa
fixed pytest_modules.yml
2022-05-24 19:19:38 -04:00
Mahesh Binzer-Panchal
3d51956b88
Merge branch 'master' into kat_hist
2022-05-24 23:10:13 +02:00
Thiseas C. Lamnidis
6d04395c3c
Merge branch 'master' into sexdeterrmine
2022-05-24 13:17:37 +02:00
Mahesh Binzer-Panchal
afb5f226e6
Merge branch 'master' into kat_hist
2022-05-24 13:06:31 +02:00
Ramprasad Neethiraj
b4982ff6e3
Merge branch 'master' into rhocall
2022-05-24 09:41:30 +02:00
SusiJo
50128b0c86
Merge branch 'master' into cnvkit_reference
2022-05-24 07:49:44 +02:00
SusiJo
8fec7ae321
added new testdata path
2022-05-23 19:01:46 +02:00
SusiJo
bbee9e3c3b
add new module cnvkit/reference
2022-05-23 18:35:50 +02:00
Thiseas Christos Lamnidis
37c6fb8fed
Merge remote-tracking branch 'upstream/master' into sexdeterrmine
2022-05-23 17:30:21 +02:00
Thiseas Christos Lamnidis
96260ced83
Add test data to config
2022-05-23 17:15:57 +02:00
SusiJo
5d5eacee63
Merge branch 'nf-core:master' into cnvkit/antitarget
2022-05-23 16:52:33 +02:00
SusiJo
4f9d672e55
added new module cnvkit/antitarget
2022-05-23 16:52:06 +02:00
FriederikeHanssen
754afa9ff3
Merge branch 'master' into gatk_filter
2022-05-23 15:37:44 +02:00
Ramprasad Neethiraj
9fb327fec7
Merge branch 'master' of https://github.com/nf-core/modules into rhocall
2022-05-23 13:06:00 +02:00
Mahesh Binzer-Panchal
e06fb752c3
Merge branch 'master' into kat_hist
2022-05-23 08:52:13 +02:00
Rike
520dd06ca3
add new testdata
2022-05-22 13:25:39 +02:00
Ramprasad Neethiraj
2542c9d176
add tests
2022-05-20 16:46:19 +02:00
Mahesh Binzer-Panchal
2926ec0abb
Add mash screen
2022-05-20 13:23:11 +00:00
Ramprasad Neethiraj
c70b169f61
create modules
2022-05-20 13:34:54 +02:00
Rike
bb3e64647b
Merge remote-tracking branch 'origin/master' into gatk_filter
2022-05-18 15:52:47 +02:00
FriederikeHanssen
44e9cf56fa
Merge branch 'master' into gatk_cnnscore
2022-05-18 15:32:36 +02:00
Rike
e8221cf98e
Merge remote-tracking branch 'origin' into gatk_cnnscore
2022-05-18 14:27:25 +02:00
James A. Fellows Yates
965fabdd54
Merge branch 'master' into motus_profile
2022-05-18 11:25:48 +01:00
Rike
15fba1dd7c
add filter variant tranches
2022-05-17 23:01:24 +02:00
Rike
05611cf27c
update pytest
2022-05-17 19:11:05 +02:00
Jose Espinosa-Carrasco
3614c19206
Merge branch 'master' into biobambam/bammerge
2022-05-17 15:07:37 +02:00
Nicolas Vannieuwkerke
6342f5b099
added bedtools split
2022-05-17 14:24:32 +02:00
Matthias De Smet
d3ddc2221a
Merge branch 'master' into biobambam/bammerge
2022-05-17 08:26:28 +02:00
Subazini TK
79c2c529fc
Merge branch 'master' into hmtnote
2022-05-17 08:05:47 +02:00
JIANHONG OU
671bacb6df
Merge branch 'master' into motus_profile
2022-05-16 17:34:49 -04:00
Matthias De Smet
d0db186e84
Merge branch 'master' into biobambam/bammerge
2022-05-16 20:52:48 +02:00
sysbiocoder
fe009b738a
modified: tests/config/pytest_modules.yml
2022-05-16 15:20:15 +00:00
Matthias De Smet
af69ea749d
add module: biobambam/bammerge
2022-05-16 14:39:58 +02:00
Veit Schwämmle
74a1c1400e
Merge branch 'master' into maxquant
2022-05-16 13:26:35 +02:00
Jasmin F
adcfae6cd4
Merge branch 'master' into antismashlite
2022-05-16 10:38:01 +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
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
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
308ab8801d
Merge branch 'master' into kat_hist
2022-05-12 16:52:05 +02:00
James A. Fellows Yates
3c02e6056c
Merge branch 'master' into antismashlite
2022-05-12 14:53:52 +02:00
Robert A. Petit III
8b6e1aff38
Merge branch 'master' into rp3-add-snippy
2022-05-11 12:28:27 -06:00
Moritz E. Beber
b2dbaa9930
refactor: rename module
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
Mahesh Binzer-Panchal
fbe2f85e7b
Fix path
2022-05-11 13:53:38 +00:00
Mahesh Binzer-Panchal
fd579ebbb3
Merge branch 'master' into kat_hist
2022-05-11 12:43:11 +02:00
