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3145 commits 30 branches 0 tags 142 MiB
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1652 commits

Author SHA1 Message Date
James Fellows Yates
4d7afa21e2 Add GATK indelrealigner tests 2022-06-08 21:14:08 +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
Ramprasad Neethiraj
1d67489056 update test 2022-06-08 16:36:02 +02:00
Ramprasad Neethiraj
0b090a6b6d Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-06-08 16:34:34 +02:00
Taniguti
d037f0ec97
Merge branch 'master' into haplocheck 2022-06-08 10:47:38 -03:00
Ramprasad Neethiraj
3cabdfac20
Merge branch 'master' into update_roh 2022-06-08 15:04:34 +02:00
Ramprasad Neethiraj
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
James A. Fellows Yates
615cb0722f
Merge branch 'master' into fix-filtlong 2022-05-31 20:25:16 +02:00
James Fellows Yates
c1ac3fbb59 Skeleton 2022-05-31 20:13:48 +02:00
James Fellows Yates
df22cd80df Fix config for tests 2022-05-31 20:07:52 +02:00
FriederikeHanssen
19037ed8f4
Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs 2022-05-31 17:42:27 +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
SusiJo
84f584875e change string array 2022-05-31 15:50:31 +02:00
James A. Fellows Yates
edc9e83a7d
Merge branch 'master' into fix-filtlong 2022-05-31 15:47:39 +02:00
James Fellows Yates
3e20ca7e9a Don't hardcode forced output names 2022-05-31 15:46:28 +02:00
SusiJo
58389e550d test json array 2022-05-31 15:41:50 +02:00
SusiJo
49135415ae
Merge branch 'master' into gatk_spark 2022-05-31 15:36:55 +02:00
SusiJo
941760f75d ran prettier 2022-05-31 15:36:02 +02:00
SusiJo
35e296cd7d added brackets 2022-05-31 15:35:34 +02:00
SusiJo
37b543e3e7 changed to tab 2022-05-31 15:29:27 +02:00
SusiJo
810564deca
Merge branch 'master' into gatk_spark 2022-05-31 15:24:58 +02:00
nvnieuwk
a6c7635b73
Merge branch 'master' into add-tbi-to-bcftools-concat 2022-05-31 15:20:03 +02:00
Nicolas Vannieuwkerke
51b0a6e4f3 Added optional input of index files to bcftools/concat 2022-05-31 15:15:58 +02:00
SusiJo
9ef09e6add adjusted newlines 2022-05-31 14:54:39 +02:00
SusiJo
205576279f ran prettier again 2022-05-31 14:50:55 +02:00
James Fellows Yates
430def06fa Switch from md5sum to string due to conda flakiness 2022-05-31 14:45:41 +02:00
SusiJo
d484aa1906 adjusted tabs 2022-05-31 14:45:23 +02:00
SusiJo
e083bfafa0 ran prettier 2022-05-31 14:38:45 +02:00
SusiJo
1e396d767f Merge remote-tracking branch 'upstream/master' into gatk_spark 2022-05-31 14:36:14 +02:00
SusiJo
ea526051a4 new test.yml 2022-05-31 14:35:42 +02:00
SusiJo
3117b2973c added test for metrics 2022-05-31 14:35:29 +02:00
SusiJo
e0e8273f74 adjusted input to use queryname sorted bams 2022-05-31 14:35:18 +02:00
James Fellows Yates
723852bf3d Fixes running without shortreads, and also ensures all tests produce non-empty fastq.gz files 2022-05-31 13:38:18 +02:00
James Fellows Yates
7ffe98ac8b Add gatk/indelrealigner 2022-05-30 21:12:21 +02:00
jtangrot
6ae405c5da prettier 2022-05-30 13:35:12 +02:00