SusiJo
efc1e1bb71
rm line
...
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-02 16:23:18 +02:00
SusiJo
44daa5d687
update prefix
...
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-02 16:23:09 +02:00
SusiJo
39e34418c9
added metrics as optional output
2022-05-31 14:34:50 +02:00
SusiJo
b34e5ea6bf
rm unnecessary spark_user
2022-05-25 16:38:48 +02:00
Rike
175ea9b7f9
fix version
2022-05-23 12:15:33 +02:00
Rike
5d72500d60
remove variables used for test data generation, add tbi
2022-05-22 13:34:56 +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
10840a0562
Conda not suported
2022-05-18 14:26:21 +02:00
Rike
5ae757121f
Add indices and meta
2022-05-17 23:38:26 +02:00
Rike
05837a011d
Add comment
2022-05-17 23:06:52 +02:00
Rike
15fba1dd7c
add filter variant tranches
2022-05-17 23:01:24 +02:00
Rike
e0fcbb428d
Add CNNScoreVariants
2022-05-17 19:09:46 +02:00
Praveen Raj S
df2620cfc7
Merge branch 'master' into process_lable_markdup
2022-05-16 15:53:26 +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
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
9d53577282
linting
2022-05-13 13:48:33 +02:00
Nicolas Vannieuwkerke
8a17b6dd0e
added gatk4/splitintervals
2022-05-13 13:46:34 +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
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
Lucpen
62c6123ec4
fix gatk4_mutect2 test by changing main.nf
2022-05-02 15:11:57 +02:00
Lucpen
dfabf960dc
Merge branch 'master' into adding_stub_to_modules
2022-05-02 14:20:03 +02:00
Lucpen
f231291e77
fix gatk4_reversam test
2022-05-02 12:58:12 +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
Lucpen
6b64f9cb6c
feat added stub to modules
2022-05-02 10:34:14 +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
Maxime U. Garcia
10ca39a86f
add intervals possibilities to splitncigarreads ( #1571 )
2022-04-27 16:03:44 +02:00
Maxime U. Garcia
e04970b7d2
typo in command line ( #1523 )
2022-04-13 15:15:44 +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
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
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
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 )
...
* 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
nickhsmith
2383d43a0f
update priority ( #1334 )
...
bumping the base resource label
2022-02-22 14:25:36 +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
nickhsmith
8717792135
include intervals_index ( #1308 )
...
* include intervals_index
In order to run the GATK `GenotypeGVCFs` tool with an interval file (such as a .bed file) you need to have the corresponding index file. Otherwise you get the following error message
```
A USER ERROR has occurred: An index is required but was not found for file genome.bed.gz: work/6c/541fce2dc670597f62a571c72288c6/genome.bed.gz. Support for unindexed block-compressed files has been temporarily disabled. Try running IndexFeatureFile on the input.
```
including the index file fixes this problem
* Update meta.yml
2022-02-16 18:35:09 +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
