Lucpen
f434d0c671
Adding stubs to PicardLiftovervcf, GATK4_mergevcfs and filterMutectCalls ( #1621 )
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* feat added stubs to picard_liftovervcf
* feat adding stubs to gatk4_mergevcfs
* feat adding stubs to gatk4_filtermutectcalls
* fix tests
* fix output name filtermutectcalls
* fix test
* fix added missing [
* Update tests/modules/gatk4/mergevcfs/test.yml
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
* Update tests/modules/gatk4/filtermutectcalls/test.yml
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
* Update tests/modules/picard/liftovervcf/test.yml
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
* Update modules/gatk4/filtermutectcalls/main.nf
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
* Update modules/gatk4/filtermutectcalls/main.nf
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
* Update modules/gatk4/mergevcfs/main.nf
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
* Update modules/gatk4/mergevcfs/main.nf
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
* Update modules/picard/liftovervcf/main.nf
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
* Trying something on picard_liftovervcf
* fix adding test data for stubs
* fix added bracket and unindented workflow
* fix picard 2.27.1 -> 2.27.0 to solve PaddingError
* Update main.nf
fix added tbi to stub
Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
2022-09-28 09:50:11 +02:00
nvnieuwk
5d8edefb26
new module gatk4/printsvevidence ( #2103 )
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* new module gatk4/printsvevidence
* linting
Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
2022-09-27 08:30:16 +02:00
nvnieuwk
65800cee75
new module gatk4/collectsvevidence ( #2039 )
2022-09-09 10:58:47 +02:00
FriederikeHanssen
e726b1730d
MD finally supports cram output ( #2019 )
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* MD finally supports cram output
* publish crai file
* fix test output
* fix mv
* figure out if contains breaks stuff
* remove variable checksum
* add contains check
* remove variable checksum
Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
2022-09-07 11:04:58 +02:00
nvnieuwk
09acfad211
new module gatk4/collectreadcounts ( #1998 )
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* added the module
* updated test.yml
* Update modules/gatk4/collectreadcounts/main.nf
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
* small fix
* tests update
* linting
* tests update (again)
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-09-05 10:49:13 +02:00
nickhsmith
edfe28a5e0
Variant recalibration ( #1885 )
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* update tests
* update
* update
* make the manta inputs consistant for germline/somatic/tumoronly
* match chromosomes to cram file (chr21)
* undo genotypegvfs
* undo genotypegvfs
* update VariantRecalibrator
* lint
* add '--resource:' tag
Co-authored-by: Smith Nicholas <smith@in.tum.de>
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-07-15 09:21:34 +02:00
Aleksei Korzhenkov
848ee9a215
Improve descriptions for modules with missing
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Description and keywords
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-07-06 12:03:08 +02:00
Adam Talbot
009f7c691c
Add module: gatk4/leftalignandtrimvariants ( #1808 )
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* Added: gatk4/leftalignandtrimvariants
Additions:
- GATK4/LeftAlignAndTrimVariants module
- Use sars-ncov2 test data as this normalises a larger INDEL correctly.
Fixes #1801
* fixup: Added index to output spec
* fixup: Pattern of tbi output corrected to 'tbi'
* gatk4/leftalignandtrimvariants: Added intervals
Changes:
- gatk4/leftalignandtrimvariants now supports optional interval as BED
file
- Tests added with and without interval. Not test BED file excludes all
variants so no variants are actually normalised.
Fixes #1801
* fixup: leftalignandtrimvariants vcf->tbi fix
* fixup: gatk4/leftalignandtrimvariants Intervals added to meta.yml
2022-06-28 10:44:08 +02:00
FriederikeHanssen
1ac223ad43
GATK/Getpileupsummaries: If no intervals use variants instead ( #1787 )
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If no intervals use variants instead
2022-06-16 15:00:01 +02:00
Maxime U. Garcia
878a5a8093
Merge branch 'master' into update_spark
2022-06-09 15:49:31 +02:00
Rike
6a4732ef3b
similar issues arise with bqsrspark, also use broadinstitute container
2022-06-09 15:29:00 +02:00
Rike
8e8f4c9c51
remove singulairty container
2022-06-09 15:16:11 +02:00
nvnieuwk
873215c8ae
Update modules/gatk4/reblockgvcf/main.nf
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-09 15:11:18 +02:00
Rike
89a6a03e38
fix container tag
2022-06-09 15:09:19 +02:00
Nicolas Vannieuwkerke
81fff7384d
small fix and typo
2022-06-09 15:08:02 +02:00
Rike
b9e397ff15
use broadinstitute container
2022-06-09 15:06:46 +02:00
nvnieuwk
bf73b6d376
Merge branch 'master' into new-module-gatk4/reblockgvcf
2022-06-09 14:57:20 +02:00
Nicolas Vannieuwkerke
fe9e4ece00
new module gatk4/reblockgvcf
2022-06-09 14:56:55 +02:00
Rike
ef5b0dd977
gatk4 version update to 4.2.6.1
2022-06-09 14:54:19 +02:00
SusiJo
cda434611f
fix conda with openjdk 1.8
2022-06-09 10:24:39 +02:00
SusiJo
e78ad2f88b
Merge remote-tracking branch 'origin' into gatk_spark
2022-06-07 14:00:26 +02:00
SusiJo
dbca9e8b36
adjusted prefix + test + authors
2022-06-07 13:58:57 +02:00
Nicolas Vannieuwkerke
4c7ef30fb6
changed to label to medium
2022-06-07 12:17:14 +02:00
Nicolas Vannieuwkerke
771425e7a0
add threads to calibratedragstrmodel
2022-06-07 12:11:18 +02:00
SusiJo
e2bb56608c
change prefix output
2022-06-03 13:50:45 +02:00
SusiJo
230224700e
change prefix
2022-06-03 13:20:45 +02:00
SusiJo
1db7771ea9
Merge branch 'nf-core:master' into gatk_spark
2022-06-03 13:17:35 +02:00
SusiJo
1b93cde9ff
Merge branch 'master' into gatk_spark
2022-06-02 16:24:39 +02:00
Nicolas Vannieuwkerke
f3c0107fa2
added optional to intervals
2022-06-02 16:24:03 +02:00
SusiJo
efc1e1bb71
rm line
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-02 16:23:18 +02:00
SusiJo
44daa5d687
update prefix
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Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
2022-06-02 16:23:09 +02:00
Nicolas Vannieuwkerke
b4b1f3b81d
add intervals to calibratedragstrmodel
2022-06-02 16:20:12 +02:00
Nicolas Vannieuwkerke
e53d091a6d
added dragstr model to haplotypecaller
2022-06-02 14:08:09 +02:00
nvnieuwk
3a49b82863
Update modules/gatk4/calibratedragstrmodel/main.nf
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Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-06-02 13:39:44 +02:00
Nicolas Vannieuwkerke
d3874bbae9
linting
2022-06-02 13:22:55 +02:00
Nicolas Vannieuwkerke
2a45d42868
added the calibratedragstrmodel module
2022-06-02 13:17:06 +02:00
Nicolas Vannieuwkerke
114a54c8d5
spaces fix
2022-06-01 09:22:09 +02:00
nvnieuwk
5b74a179c3
Update modules/gatk4/composestrtablefile/main.nf
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Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
2022-06-01 09:14:08 +02:00
nvnieuwk
e4f51d6f59
Merge branch 'master' into new-module-gatk4/ComposeSTRTableFile
2022-06-01 08:59:19 +02:00
asp8200
4199a05aeb
Removing redundant empty line
2022-05-31 15:34:34 +00:00
Nicolas Vannieuwkerke
80366924fd
added gatk4/composestrtablefile
2022-05-31 16:08:13 +02:00
Anders Sune Pedersen
5513d095f5
Adding tbi-files to the output from GATK4_MERGEVCFS. #1709
2022-05-31 15:37:26 +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
