Taniguti
|
547f483b74
|
Merge branch 'master' into haplocheck
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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 |
|
jasmezz
|
088b5b14f6
|
Merge branch 'r-ampir' of github.com:jasmezz/modules into r-ampir
|
2022-06-10 12:54:47 +02:00 |
|
jasmezz
|
39388abc04
|
Add file name collision check + TSV output
|
2022-06-10 12:54:39 +02:00 |
|
Alexander Peltzer
|
a0747b1405
|
Remove empty file md5sum
|
2022-06-10 11:53:28 +02:00 |
|
Alexander Peltzer
|
63f47551a8
|
Fix empty test having md5sum
|
2022-06-10 11:52:30 +02:00 |
|
Alexander Peltzer
|
1fbe69cfcc
|
Updated and fixed tests
|
2022-06-10 11:46:23 +02:00 |
|
Alexander Peltzer
|
8dfe8b795f
|
Merge remote-tracking branch 'refs/remotes/origin/cellranger-7.0.0' into cellranger-7.0.0
|
2022-06-10 11:23:15 +02:00 |
|
Alexander Peltzer
|
4928dfad34
|
Trying to fix tests
|
2022-06-10 11:22:45 +02:00 |
|
Alexander Peltzer
|
570a43ba4c
|
Fix tests
|
2022-06-10 11:21:03 +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
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2022-06-09 19:28:37 +02:00 |
|
jasmezz
|
5841f11edb
|
Replace MD5 with contains check
|
2022-06-09 18:15:27 +02:00 |
|
jasmezz
|
ecf1d146ab
|
Add full user options for AMPir
|
2022-06-09 16:59:00 +02:00 |
|
Maxime U. Garcia
|
878a5a8093
|
Merge branch 'master' into update_spark
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2022-06-09 15:49:31 +02:00 |
|
Rike
|
30262d1fdd
|
remove variable checksum
|
2022-06-09 15:44:12 +02:00 |
|
Rike
|
a5583143c4
|
update checksum
|
2022-06-09 15:38:28 +02:00 |
|
jasmezz
|
ba53e09b64
|
Implement suggestions from code review
|
2022-06-09 15:37:35 +02:00 |
|
Rike
|
95633c6853
|
update checksum
|
2022-06-09 15:30:47 +02:00 |
|
Nicolas Vannieuwkerke
|
c50df9ad04
|
fix test.yml
|
2022-06-09 15:14:37 +02:00 |
|
Nicolas Vannieuwkerke
|
81fff7384d
|
small fix and typo
|
2022-06-09 15:08:02 +02:00 |
|
Nicolas Vannieuwkerke
|
14d38e43cf
|
fix test.yml
|
2022-06-09 14:58:20 +02:00 |
|
nvnieuwk
|
bf73b6d376
|
Merge branch 'master' into new-module-gatk4/reblockgvcf
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2022-06-09 14:57:20 +02:00 |
|
Nicolas Vannieuwkerke
|
fe9e4ece00
|
new module gatk4/reblockgvcf
|
2022-06-09 14:56:55 +02:00 |
|
nvnieuwk
|
6d10909e9f
|
Update tests/modules/ensemblvep/main.nf
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
|
2022-06-09 11:55:41 +02:00 |
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nvnieuwk
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e88a4ff70b
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Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep
|
2022-06-09 11:54:22 +02:00 |
|
Nicolas Vannieuwkerke
|
e60323b757
|
typo
|
2022-06-09 11:53:59 +02:00 |
|
Nicolas Vannieuwkerke
|
7947bc662c
|
added an extra test without fasta
|
2022-06-09 11:53:16 +02:00 |
|
Nicolas Vannieuwkerke
|
a3202e41ec
|
prettier
|
2022-06-09 11:47:24 +02:00 |
|
Nicolas Vannieuwkerke
|
5ccf6fbcc9
|
add optional fasta argument to ensemblvep
|
2022-06-09 11:45:27 +02:00 |
|
SusiJo
|
0204d2374b
|
Merge remote-tracking branch 'origin/master' into gatk_spark
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2022-06-09 09:33:17 +02:00 |
|
James Fellows Yates
|
4d7afa21e2
|
Add GATK indelrealigner tests
|
2022-06-08 21:14:08 +02:00 |
|
James A. Fellows Yates
|
1fc0d3de4b
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Merge branch 'gatk3-indelrealigner' into upstream-for-indel
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2022-06-08 20:30:19 +02:00 |
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James A. Fellows Yates
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4a2157e5ab
|
Merge branch 'master' into gatk-realigntargetcreator
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2022-06-08 20:15:02 +02:00 |
|
Taniguti
|
89bffe3a5e
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Merge branch 'master' into haplocheck
|
2022-06-08 15:00:06 -03:00 |
|
Ramprasad Neethiraj
|
1d67489056
|
update test
|
2022-06-08 16:36:02 +02:00 |
|
Ramprasad Neethiraj
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0b090a6b6d
|
Merge branch 'master' of https://github.com/nf-core/modules into rhocall
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2022-06-08 16:34:34 +02:00 |
|
Taniguti
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d037f0ec97
|
Merge branch 'master' into haplocheck
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2022-06-08 10:47:38 -03:00 |
|
Ramprasad Neethiraj
|
3cabdfac20
|
Merge branch 'master' into update_roh
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2022-06-08 15:04:34 +02:00 |
|
Ramprasad Neethiraj
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c079ee2025
|
fix test
|
2022-06-08 14:48:16 +02:00 |
|
Matthias De Smet
|
c005a5e007
|
formatting
|
2022-06-08 14:42:58 +02:00 |
|
Matthias De Smet
|
100b3f244c
|
Apply suggestions from code review
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
|
2022-06-08 14:24:55 +02:00 |
|
Lucas Taniguti
|
b2afb3b2ee
|
fix: string interpolation and test input access
|
2022-06-08 09:08:59 -03:00 |
|
Matthias De Smet
|
71e3056813
|
Merge branch 'master' into update/multiqc
|
2022-06-08 14:03:26 +02:00 |
|
Matthias De Smet
|
439d2a9e67
|
update mqc inputs
|
2022-06-08 13:48:27 +02:00 |
|
Lucas Taniguti
|
abaec30889
|
tests: add stub
|
2022-06-08 08:46:22 -03:00 |
|
Lucas Taniguti
|
f26979c44e
|
tests: add input to test_data.config
|
2022-06-08 08:10:25 -03:00 |
|
Taniguti
|
d5e077a2e9
|
Merge branch 'master' into haplocheck
|
2022-06-08 07:31:28 -03:00 |
|
Maxime U. Garcia
|
7230bf2174
|
Merge branch 'master' into update_tiddit
|
2022-06-08 11:16:01 +02:00 |
|
Taniguti
|
3be549534d
|
Apply suggestions from code review
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
|
2022-06-07 14:09:04 -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 |
|
SusiJo
|
745e47cd33
|
add versions.yml
|
2022-06-07 14:38:43 +02:00 |
|
Ramprasad Neethiraj
|
65a0fb959f
|
rhocall
|
2022-06-07 14:37:03 +02:00 |
|
SusiJo
|
e78ad2f88b
|
Merge remote-tracking branch 'origin' into gatk_spark
|
2022-06-07 14:00:26 +02:00 |
|
Matthias De Smet
|
bffd1c562b
|
Merge branch 'master' into update/multiqc
|
2022-06-07 13:59:00 +02:00 |
|
SusiJo
|
dbca9e8b36
|
adjusted prefix + test + authors
|
2022-06-07 13:58:57 +02:00 |
|
Matthias De Smet
|
e5bf87aec3
|
possible fix for name collisions
|
2022-06-07 13:58:27 +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 |
|
Nicolas Vannieuwkerke
|
771425e7a0
|
add threads to calibratedragstrmodel
|
2022-06-07 12:11:18 +02:00 |
|
SusiJo
|
1368956d88
|
Merge remote-tracking branch 'origin/master' into gatk_spark
|
2022-06-07 11:00:33 +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 |
|
MaxUlysse
|
97e66015ca
|
add test + fix issues
|
2022-06-03 15:51:02 +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 |
|
MaxUlysse
|
f1a5cc07db
|
restructure tiddit/sv + test (just one for now)
|
2022-06-03 13:00:29 +02:00 |
|
MaxUlysse
|
40996cdbe1
|
update tiddit/cov + more tests
|
2022-06-03 12:07:16 +02:00 |
|
MaxUlysse
|
36ffd4fbf7
|
Merge remote-tracking branch 'upstream/master' into update_tiddit
|
2022-06-03 11:38:33 +02:00 |
|
Rike
|
2c9e2f5e73
|
Update TIDDIT to 3.0.0
|
2022-06-03 10:52:50 +02:00 |
|
James Fellows Yates
|
a565d9072a
|
Add GATK UnifiedGenotyper
|
2022-06-02 21:39:39 +02:00 |
|
James Fellows Yates
|
544b62df45
|
Star work on GATK UG
|
2022-06-02 21:11:17 +02:00 |
|
James Fellows Yates
|
9a4f22e8d1
|
Merge branch 'gatk-realigntargetcreator' of github.com:jfy133/nf-core-modules into gatk-realigntargetcreator
|
2022-06-02 20:32:03 +02:00 |
|
James Fellows Yates
|
c469a2b35e
|
Fux tests
|
2022-06-02 20:32:00 +02:00 |
|
James A. Fellows Yates
|
abc619a3e2
|
Merge branch 'master' into gatk-realigntargetcreator
|
2022-06-02 20:24:24 +02:00 |
|
SusiJo
|
1b93cde9ff
|
Merge branch 'master' into gatk_spark
|
2022-06-02 16:24:39 +02:00 |
|
Nicolas Vannieuwkerke
|
b4b1f3b81d
|
add intervals to calibratedragstrmodel
|
2022-06-02 16:20:12 +02:00 |
|
nvnieuwk
|
e107d61069
|
Update tests/modules/gatk4/haplotypecaller/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
|
2022-06-02 14:20:15 +02:00 |
|
nvnieuwk
|
e419d306df
|
Update tests/modules/gatk4/haplotypecaller/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
|
2022-06-02 14:20:10 +02:00 |
|
nvnieuwk
|
2ce1cf3329
|
Update tests/modules/gatk4/haplotypecaller/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
|
2022-06-02 14:20:04 +02:00 |
|
nvnieuwk
|
a6c4276ad7
|
Update tests/modules/gatk4/haplotypecaller/test.yml
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
|
2022-06-02 14:19:57 +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 |
|
nvnieuwk
|
eadab8e002
|
Merge branch 'master' into new-module-gatk4/CalibrateDragstrModel
|
2022-06-02 13:18:36 +02:00 |
|
Nicolas Vannieuwkerke
|
2a45d42868
|
added the calibratedragstrmodel module
|
2022-06-02 13:17:06 +02:00 |
|
SusiJo
|
2f3ddc90fb
|
added fasta_fai as input + changed if statements
|
2022-06-02 12:57:50 +02:00 |
|
Matthias De Smet
|
51be617b1c
|
fix untar output dir
|
2022-06-02 11:09:55 +02:00 |
|
SusiJo
|
7742661784
|
Merge remote-tracking branch 'upstream/master' into cnvkit_bam
|
2022-06-02 10:51:43 +02:00 |
|
SusiJo
|
a21cfb666e
|
changed container + add cram2bam conversion
|
2022-06-02 10:38:05 +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 |
|
Nicolas Vannieuwkerke
|
8470f3cb7e
|
linting
|
2022-06-01 09:20:20 +02:00 |
|
James A. Fellows Yates
|
5a94794793
|
Merge branch 'master' into r-ampir
|
2022-06-01 09:18:54 +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 |
|
Alexander Peltzer
|
9ac3cf342a
|
Merge branch 'master' into gatk-realigntargetcreator
|
2022-05-31 21:12:59 +02:00 |
|
James Fellows Yates
|
7633d7816b
|
Add GATK(3)/realignertargetcreator
|
2022-05-31 20:35:54 +02:00 |
|