Nicolas Vannieuwkerke
8470f3cb7e
linting
2022-06-01 09:20:20 +02:00
Nicolas Vannieuwkerke
d4f3df4677
Updated the test
2022-06-01 09:17:05 +02:00
nvnieuwk
e4f51d6f59
Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile
2022-06-01 08:59:19 +02:00
Nicolas Vannieuwkerke
1166fb5150
prettier
2022-05-31 16:13:38 +02:00
Nicolas Vannieuwkerke
ec41ea6082
fix test.yml
2022-05-31 16:12:05 +02:00
Nicolas Vannieuwkerke
80366924fd
added gatk4/composestrtablefile
2022-05-31 16:08:13 +02:00
asp8200
98bb45cf4e
Updating test for gatk4/mergevcfs
2022-05-31 13:59:56 +00:00
Rike
e34dcdd8bc
add brackets to contains
2022-05-23 13:19:42 +02:00
Rike
dc6ad1bff6
add brackets to contains
2022-05-23 13:07:08 +02:00
Rike
093e3aafdd
contains
2022-05-23 13:04:49 +02:00
Rike
a8de9fd085
test path update
2022-05-23 12:53:36 +02:00
Rike
3af61cfbbc
fix input cardinality for index
2022-05-23 12:26:12 +02:00
Rike
a8dac59c50
md5sum not consistent
2022-05-23 12:10:50 +02:00
Rike
2f36a44f61
nf-core create-test-yml
2022-05-23 12:00:31 +02:00
Rike
cd60b4c6eb
add in testdata paths
2022-05-22 13:35:35 +02:00
Rike
bb3e64647b
Merge remote-tracking branch 'origin/master' into gatk_filter
2022-05-18 15:52:47 +02:00
Rike
e8221cf98e
Merge remote-tracking branch 'origin' into gatk_cnnscore
2022-05-18 14:27:25 +02:00
Rike
5ae757121f
Add indices and meta
2022-05-17 23:38:26 +02:00
Rike
15fba1dd7c
add filter variant tranches
2022-05-17 23:01:24 +02:00
Rike
afa0f2a995
update test
2022-05-17 22:53:41 +02:00
Rike
265fd882ca
update test
2022-05-17 19:44:48 +02:00
Rike
5f63904a50
update test
2022-05-17 19:37:18 +02:00
Rike
e0fcbb428d
Add CNNScoreVariants
2022-05-17 19:09:46 +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
Nicolas Vannieuwkerke
a72f06dfe8
removed versions checksum
2022-05-13 14:27:59 +02:00
Nicolas Vannieuwkerke
8a17b6dd0e
added gatk4/splitintervals
2022-05-13 13:46:34 +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
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
Lucpen
971a17a3ab
fix datatest for stubs
2022-05-06 15:34:18 +02:00
Lucpen
0fa36e6777
fix added correct entry workflow in test.yml
2022-05-06 15:26:34 +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
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
Lucpen
de40c1bf54
chore removing file from test
2022-05-02 13:15:01 +02:00
Lucpen
08d5acbeb6
feat added tests for stubs
2022-05-02 11:59:08 +02:00
Maxime U. Garcia
10ca39a86f
add intervals possibilities to splitncigarreads ( #1571 )
2022-04-27 16:03:44 +02:00
Maxime U. Garcia
409af2f27c
Improve syntax/logic coherence in all gatk4 plugins ( #1459 )
...
* 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
James A. Fellows Yates
e080f4c8ac
Untar unzip meta ( #1408 )
...
* 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
Edmund Miller
f080015754
Prettier ( #1405 )
...
* 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
Michael J Cipriano
6400317623
Gatk4 selectvariants ( #1346 )
...
* initial commit
* tested
Co-authored-by: Cipriano <rrn8@cdc.gov>
Co-authored-by: Sateesh <33637490+sateeshperi@users.noreply.github.com>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-24 09:51:48 +01:00
Sateesh
a25423dbb9
Gatk4 combinegvcfs ( #1342 )
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* add gatk4/combinegvcfs module
* update gatk4/combinegvcfs
* loop to create a string adding -V to each vcf file
* add contains for variable md5
* rm whitespace
* meta in output
* fix indentations
* fix indentations
* move tmpdir to args and update conda version
Co-authored-by: Peri <rrx8@cdc.gov>
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-02-23 16:29:29 +01:00
FriederikeHanssen
3f364e2f31
add mergemutectstats ( #1314 )
...
* add mergemutectstats
* correct md5sum
* Update modules/gatk4/mergemutectstats/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-02-18 09:38:55 +01:00
FriederikeHanssen
fcd483e1b5
intervallisttobed ( #1312 )
...
* intervallisttobed
* correct md5sum
2022-02-17 16:32:26 +01:00
FriederikeHanssen
8c8be7d7c6
Add gatherpileupsummaries ( #1311 )
...
* Add gatherpileupsummaries
* fix checksum
* Update modules/gatk4/gatherpileupsummaries/main.nf
* Add in when
2022-02-17 15:05:21 +01:00
Matthias Hörtenhuber
e745e167c1
Fix formatting in yaml files, add yamllint config ( #1279 )
...
* fix yml formatting
* allow fastq.gz and fq.gz as file input, add meta.yml and test
* fix yaml files
* Revert "allow fastq.gz and fq.gz as file input, add meta.yml and test"
This reverts commit 34002d7a7a8c7f7bb4600c3377f35c87849f71a4.
* prettier magic!
* fix comments for yamllint
* remove node version number
* fix linting errors
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2022-02-15 11:15:27 +00:00
