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1479 commits

Author SHA1 Message Date
Mahesh Binzer-Panchal
e91e99db30
Add GeneScopeFK (#1781) 2022-06-14 20:49:06 +02:00
Mahesh Binzer-Panchal
8ded6d441a
Add MerquryFK (#1778) 
* Add MerquryFK

* Change resource allocation
 2022-06-14 16:36:02 +02:00
Mahesh Binzer-Panchal
fd5aea0b76
Add FastK/Histex (#1776) 2022-06-14 16:30:37 +02:00
nvnieuwk
1a4ab76618
new module rtgtools/pedfilter (#1777) 
* new module rtgtools/pedfilter

* removed checksum due to the presence of a date in the file
 2022-06-14 16:02:18 +02:00
Mahesh Binzer-Panchal
4e308c131e
FastK/fastK (#1739) 
* Add FastK/FastK

* Add ktab and prof outputs

* Add the hidden files necessary for the optional files

* Update image

* Apply suggestions from code review

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>

Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
 2022-06-14 13:39:52 +02:00
Thomas A. Christensen II
8b2a473f58
New module: krakentools/kreport2krona (#1746) 
* Add module definition for kreport2krona

* Add metadata for kreport2krona module

* Add tests for kreport2krona

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
 2022-06-13 20:14:44 +02:00
Maxime U. Garcia
b689b8ed88
TIDDIT - add --skip_assembly when no bwa specified (#1769) 
add --skip_assembly when no bwa specified
 2022-06-13 17:02:59 +02:00
Maxime U. Garcia
680b6c5b04
Update tiddit to 3.1.0 (#1767) 
* update TIDDIT to 3.1.0

* update VCF too as version is in file
 2022-06-13 16:24:34 +02:00
Merlin Szymanski
8f199c4fa4
Create atlas/splitmerge Module (#1756) 
* Add atlas/splitmerge module

* Finish the tests for atlas/splitmerge

* Prettier

* Update modules/atlas/splitmerge/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Remove curly brackets from meta.yml parameters

For single-file outputs, as reviewed

* Lintung: Remove trailing white-space

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-13 15:09:32 +02:00
Robert A. Petit III
81232af296
add module for mcroni (#1750) 
Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
 2022-06-13 15:04:01 +02:00
WackerO
f1b3174501
Merge branch 'master' into mpileup_bgzip 2022-06-13 09:48:47 +02:00
WackerO
24e05f6097
Update modules/samtools/mpileup/main.nf 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-06-13 09:35:34 +02:00
FriederikeHanssen
5b27af025a
Merge branch 'master' into manta_convert 2022-06-13 09:29:50 +02:00
FriederikeHanssen
b8ff8e32e3
Update modules/manta/convertinversion/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-13 09:26:29 +02:00
WackerO
c3b6ec8f3b Merge branch 'master' of https://github.com/nf-core/modules into mpileup_bgzip 2022-06-13 08:31:01 +02:00
WackerO
dc6c09e083 samtools mpileup now bgzips mpileup files 2022-06-11 13:32:53 +02:00
Rike
dd6c514710 Fix linting 2022-06-11 13:12:56 +02:00
Rike
650076cacf add manta conversion script 2022-06-11 13:01:18 +02:00
Taniguti
547f483b74
Merge branch 'master' into haplocheck 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
James A. Fellows Yates
01d4a1fa3a
Apply suggestions from code review 2022-06-10 14:46:58 +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
Gisela Gabernet
5a16cf7bae
Merge branch 'master' into cellranger-7.0.0 2022-06-10 11:19:57 +02:00
Alexander Peltzer
62c4b59d10
Update main.nf 2022-06-10 11:05:59 +02:00
Thiseas C. Lamnidis
9948e9fe21
Merge branch 'master' into sexdeterrmine 2022-06-10 11:03:18 +02:00
Thiseas C. Lamnidis
fe855a1c23
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-06-10 11:03:01 +02:00
Alexander Peltzer
cfcd93f3e7
Update Dockerfile 2022-06-10 10:56:13 +02:00
Alexander Peltzer
61d87bb2bc
Update main.nf 2022-06-10 10:54:06 +02:00
Alexander Peltzer
e499abe572
Update main.nf 2022-06-10 10:53:48 +02:00
Alexander Peltzer
8032833e6e
Update main.nf 2022-06-10 10:53:09 +02:00
Alexander Peltzer
e36b79201d
Update Dockerfile 2022-06-10 10:52:13 +02:00
James A. Fellows Yates
c9db677a45
Merge branch 'master' into r-ampir 2022-06-09 19:28:37 +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 2022-06-09 15:49:31 +02:00
jasmezz
ba53e09b64 Implement suggestions from code review 2022-06-09 15:37:35 +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 
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
nvnieuwk
e88a4ff70b
Merge branch 'master' into add-optional-fasta-parameter-to-ensemblvep 2022-06-09 11:54:22 +02:00
Nicolas Vannieuwkerke
5ccf6fbcc9 add optional fasta argument to ensemblvep 2022-06-09 11:45:27 +02:00
SusiJo
cda434611f fix conda with openjdk 1.8 2022-06-09 10:24:39 +02:00
SusiJo
0204d2374b Merge remote-tracking branch 'origin/master' into gatk_spark 2022-06-09 09:33:17 +02:00
James A. Fellows Yates
70f7f07a37
Apply suggestions from code review 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-06-09 08:33:37 +02:00
James Fellows Yates
939653a47e Changes after code review 2022-06-09 08:26:04 +02:00
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
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
Lucas Taniguti
f5615c3db6 fix: stub output name 2022-06-08 10:10:24 -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
e5f8924fab
Update modules/multiqc/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 14:41:10 +02:00
Ramprasad Neethiraj
ea4dc866e0 add index 2022-06-08 14:38:55 +02:00
Ramprasad Neethiraj
1648d2fcba add index 2022-06-08 14:36:25 +02:00
Matthias De Smet
7b018acabb
Update modules/multiqc/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 14:36:13 +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
f1e33ca6e0 update mqc command 2022-06-08 14:02:04 +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
Taniguti
d5e077a2e9
Merge branch 'master' into haplocheck 2022-06-08 07:31:28 -03:00
MaxUlysse
07eff4346f fix path to symbolic links 2022-06-08 11:46:45 +02:00
Maxime U. Garcia
4935bb98cb
Apply suggestions from code review 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-06-08 11:38:02 +02:00
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
Matthias De Smet
d196552e06 update input 2022-06-07 16:33:17 +02:00
Ramprasad Neethiraj
16e5e6093c Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-06-07 14:45:09 +02:00
Ramprasad Neethiraj
17a4e93142 fix versions.yaml 2022-06-07 14:43:35 +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
Nicolas Vannieuwkerke
4c7ef30fb6 changed to label to medium 2022-06-07 12:17:14 +02:00
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
0d087b4890
Update modules/gatk/realignertargetcreator/main.nf 2022-06-03 21:33:54 +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
James A. Fellows Yates
e827a042ce
Update modules/gatk/unifiedgenotyper/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-06-03 21:24:03 +02:00
Robert A. Petit III
d7cec801b2
Update main.nf 2022-06-03 13:05:43 -06:00
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
MaxUlysse
f9ac4e28e9 cover all use cases 2022-06-03 15:37:10 +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
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
Matthias De Smet
cf9d62fc83
Merge branch 'master' into bump/picard 2022-06-02 22:09:42 +02:00
James Fellows Yates
a565d9072a Add GATK UnifiedGenotyper 2022-06-02 21:39:39 +02:00
James Fellows Yates
a14855dbe8 Start meta 2022-06-02 21:22:21 +02:00
James Fellows Yates
544b62df45 Star work on GATK UG 2022-06-02 21:11:17 +02:00
James Fellows Yates
de88adc926 Standardise parameters (no tests yet until realigntarget creator ready) 2022-06-02 20:35:34 +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 Fellows Yates
599b264280 Standaridse parameters 2022-06-02 20:27:16 +02:00
James A. Fellows Yates
b1edcc6e94
Update modules/gatk/realignertargetcreator/main.nf 2022-06-02 20:26:09 +02:00
James A. Fellows Yates
43ef3841d1
remove duplciate path 2022-06-02 20:25:12 +02:00
James A. Fellows Yates
abc619a3e2
Merge branch 'master' into gatk-realigntargetcreator 2022-06-02 20:24:24 +02:00
James Fellows Yates
28101149b6 Merge branch 'gatk-realigntargetcreator' of github.com:jfy133/nf-core-modules into gatk-realigntargetcreator 2022-06-02 20:24:17 +02:00
James Fellows Yates
14c63f9ccc Changes after review 2022-06-02 20:24:14 +02:00
SusiJo
1b93cde9ff
Merge branch 'master' into gatk_spark 2022-06-02 16:24:39 +02:00
Nicolas Vannieuwkerke
b028e57588 Merge branch 'add-intervals-to-calibratedragstrmodel' of github.com:nvnieuwk/modules into add-intervals-to-calibratedragstrmodel 2022-06-02 16:24:06 +02:00
Nicolas Vannieuwkerke
f3c0107fa2 added optional to intervals 2022-06-02 16:24:03 +02:00
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
nvnieuwk
897de827ee
Merge branch 'master' into add-intervals-to-calibratedragstrmodel 2022-06-02 16:20:41 +02:00
Nicolas Vannieuwkerke
b4b1f3b81d add intervals to calibratedragstrmodel 2022-06-02 16:20:12 +02:00
MaxUlysse
b623ff5d27 fix comments 2022-06-02 16:11:45 +02:00
MaxUlysse
bc0f52bcd3 fix cache version 2022-06-02 16:11:11 +02:00
MaxUlysse
046fa39582 update VEP version + cache 2022-06-02 16:09:09 +02:00
Nicolas Vannieuwkerke
e53d091a6d added dragstr model to haplotypecaller 2022-06-02 14:08:09 +02:00
Matthias De Smet
db0dc81b81
Merge branch 'master' into bump/picard 2022-06-02 13:49:03 +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
nvnieuwk
3a49b82863
Update modules/gatk4/calibratedragstrmodel/main.nf 
Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
 2022-06-02 13:39:44 +02:00
Matthias De Smet
f58771c47f
Merge branch 'master' into update/untar 2022-06-02 13:38:53 +02:00
Nicolas Vannieuwkerke
631bf7749a Merge branch 'new-module-gatk4/CalibrateDragstrModel' of github.com:nvnieuwk/modules into new-module-gatk4/CalibrateDragstrModel 2022-06-02 13:22:57 +02:00
Nicolas Vannieuwkerke
d3874bbae9 linting 2022-06-02 13:22:55 +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
45f3795670
Merge branch 'master' into bump/picard 2022-06-02 11:33:26 +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
114a54c8d5 spaces fix 2022-06-01 09:22:09 +02:00
James A. Fellows Yates
5a94794793
Merge branch 'master' into r-ampir 2022-06-01 09:18:54 +02:00
nvnieuwk
5b74a179c3
Update modules/gatk4/composestrtablefile/main.nf 
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
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
d39ba08e02 Prepare main module code 2022-05-31 20:19:49 +02:00
James Fellows Yates
c1ac3fbb59 Skeleton 2022-05-31 20:13:48 +02:00
FriederikeHanssen
19037ed8f4
Merge branch 'master' into get_tbi_files_from_gatk4_mergevcfs 2022-05-31 17:42:27 +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
James Fellows Yates
089f761f0b Actually add the changes 2022-05-31 15:49:57 +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
49135415ae
Merge branch 'master' into gatk_spark 2022-05-31 15:36:55 +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
James A. Fellows Yates
0b895871d7
Merge branch 'master' into fix-filtlong 2022-05-31 14:49:44 +02:00
SusiJo
1e396d767f Merge remote-tracking branch 'upstream/master' into gatk_spark 2022-05-31 14:36:14 +02:00
SusiJo
39e34418c9 added metrics as optional output 2022-05-31 14:34:50 +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
Sébastien Guizard
a3ae526521
Merge branch 'master' into bamtools/convert/remove_TODO 2022-05-30 17:36:36 +01:00
Sebastien Guizard
d463cd5dd6 👌 IMPROVE: Remove last TODO 2022-05-30 17:26:51 +01:00
jtangrot
5f0d75bb37 Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global 2022-05-30 13:05:00 +02:00
Jeanette Tångrot
69e00b55d3
Update modules/vsearch/usearchglobal/main.nf 
Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
 2022-05-30 13:03:45 +02:00
jtangrot
c67c15f243 Make input tuple 2022-05-30 13:01:06 +02:00
Matthias De Smet
63db63757c bump picard versions 2022-05-30 10:15:40 +02:00
jtangrot
2e16c90fce Fix whitespace 2022-05-30 09:57:05 +02:00
jtangrot
01d86439f5 Add idcutoff as input 2022-05-30 08:50:27 +02:00
jtangrot
589ce2d73a Add options for output file type 2022-05-30 08:50:27 +02:00
jtangrot
1c99ffd876 Add vserach usearch_global 2022-05-30 08:50:27 +02:00
Harshil Patel
fb6c7bca3d Bump container version for STAR to 2.7.10a 2022-05-27 11:35:04 +01:00
Sateesh Peri
ead3679829
Merge branch 'master' into rp3-add-snippy 2022-05-26 03:04:19 -04:00
Harshil Patel
72a31b76eb
Update main.nf 2022-05-25 19:42:15 +01:00
Matthias De Smet
bc7002b0c9
Merge branch 'master' into update/mosdepth 2022-05-25 19:20:45 +02:00
Matthias De Smet
72ff2732e3 add all remaining outputs to mosdepth 2022-05-25 19:19:39 +02:00
Mahesh Binzer-Panchal
3d532405a5
Merge branch 'master' into mash_screen_patch 2022-05-25 16:51:42 +02:00
SusiJo
b34e5ea6bf rm unnecessary spark_user 2022-05-25 16:38:48 +02:00
Mahesh Binzer-Panchal
c452f56289 Patch mash screen 2022-05-25 12:29:14 +00:00
jasmezz
77b5986463 Create ampir module 2022-05-25 13:27:10 +02:00
Jill V. Hagey, PhD
b1dd1d8a52
Merge branch 'nf-core:master' into gamma-update 2022-05-24 19:28:06 -04:00
Mahesh Binzer-Panchal
3d51956b88
Merge branch 'master' into kat_hist 2022-05-24 23:10:13 +02:00
jvhagey
b8aaea7429 updating paths in test.yml 2022-05-24 16:27:00 -04:00
jvhagey
f1fc7fc38e adding upzip 2022-05-24 15:15:07 -04:00
Ramprasad Neethiraj
fe90615f57 Merge branch 'rhocall' of github.com:genomic-medicine-sweden/modules into rhocall 2022-05-24 16:17:59 +02:00
Ramprasad Neethiraj
b0dba3ee75 update description 2022-05-24 16:17:15 +02:00
Ramprasad Neethiraj
c91947f8a1
Merge branch 'master' into rhocall 2022-05-24 16:07:55 +02:00
Mahesh Binzer-Panchal
9a5d6a815b
Merge branch 'master' into kat_hist 2022-05-24 15:46:12 +02:00
SusiJo
3077e4d34c
Merge branch 'master' into cnvkit/reference 2022-05-24 15:00:29 +02:00
SusiJo
8208140d21 missing meta.id changed 2022-05-24 14:59:52 +02:00
SusiJo
6b425735b9 Merge remote-tracking branch 'origin/master' into cnvkit/reference 2022-05-24 14:20:55 +02:00
SusiJo
749edce069 add prefix 2022-05-24 14:20:19 +02:00
Mahesh Binzer-Panchal
c8ffecfe86
Merge branch 'master' into kat_hist 2022-05-24 13:57:45 +02:00
Matthias De Smet
c51c047b2e
Merge branch 'master' into update/mosdepth 2022-05-24 13:50:22 +02:00
Matthias De Smet
a2a8e09762
Update modules/mosdepth/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-24 13:45:52 +02:00
Thiseas C. Lamnidis
6d04395c3c
Merge branch 'master' into sexdeterrmine 2022-05-24 13:17:37 +02:00
Mahesh Binzer-Panchal
afb5f226e6
Merge branch 'master' into kat_hist 2022-05-24 13:06:31 +02:00
Matthias De Smet
858cbe80c6 add must fail test 2022-05-24 12:43:49 +02:00
Matthias De Smet
7e777c6626 add error is is provided twice 2022-05-24 12:25:31 +02:00
Matthias De Smet
b5850fd471 add stub 2022-05-24 12:16:03 +02:00
Harshil Patel
393f23274d
Merge branch 'master' into cnvkit/reference 2022-05-24 11:14:50 +01:00
Harshil Patel
29a4f112be
Update main.nf 2022-05-24 11:14:32 +01:00
Matthias De Smet
01fb8851c3 mosdept: cram compatiblility 2022-05-24 11:47:58 +02:00
Harshil Patel
ec141dba08
Merge branch 'master' into umitools 2022-05-24 09:23:20 +01:00
SusiJo
5db94ea0ee changed tag of module 2022-05-24 10:17:41 +02:00
Ramprasad Neethiraj
b4982ff6e3
Merge branch 'master' into rhocall 2022-05-24 09:41:30 +02:00
SusiJo
0f0d555f96
Merge branch 'master' into cnvkit_reference 2022-05-24 08:03:44 +02:00
SusiJo
0708f343de
Merge branch 'master' into cnvkit_bam 2022-05-24 07:49:51 +02:00
SusiJo
50128b0c86
Merge branch 'master' into cnvkit_reference 2022-05-24 07:49:44 +02:00
SusiJo
63c038ad68
Merge branch 'nf-core:master' into cnvkit_bam 2022-05-24 07:37:24 +02:00
SusiJo
b3e2f70651
Merge branch 'master' into cnvkit/antitarget 2022-05-24 07:36:07 +02:00
SusiJo
33a72367c6
Merge branch 'nf-core:master' into cnvkit_reference 2022-05-24 07:30:29 +02:00
Harshil Patel
84f02a08a5 Update umitools/dedup module to make --output-stats optional 2022-05-23 22:31:09 +01:00
Sateesh Peri
da0ead705e
Merge branch 'master' into update/picard 2022-05-23 13:38:18 -04:00
SusiJo
58c5ec2f4e
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:53:28 +02:00
SusiJo
86b5951c14
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:48:30 +02:00
SusiJo
24905e26e2
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:48:13 +02:00
SusiJo
ddb964a4bf
rm line 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-23 18:48:04 +02:00
SusiJo
bbee9e3c3b add new module cnvkit/reference 2022-05-23 18:35:50 +02:00
Thiseas Christos Lamnidis
37c6fb8fed Merge remote-tracking branch 'upstream/master' into sexdeterrmine 2022-05-23 17:30:21 +02:00
SusiJo
5d5eacee63
Merge branch 'nf-core:master' into cnvkit/antitarget 2022-05-23 16:52:33 +02:00
SusiJo
4f9d672e55 added new module cnvkit/antitarget 2022-05-23 16:52:06 +02:00
FriederikeHanssen
754afa9ff3
Merge branch 'master' into gatk_filter 2022-05-23 15:37:44 +02:00
Ramprasad Neethiraj
9fb327fec7 Merge branch 'master' of https://github.com/nf-core/modules into rhocall 2022-05-23 13:06:00 +02:00
Rike
175ea9b7f9 fix version 2022-05-23 12:15:33 +02:00
SusiJo
fd31f64266
Merge branch 'master' into cnvkit_bam 2022-05-23 11:31:56 +02:00
Mahesh Binzer-Panchal
e06fb752c3
Merge branch 'master' into kat_hist 2022-05-23 08:52:13 +02:00
Rike
5d72500d60 remove variables used for test data generation, add tbi 2022-05-22 13:34:56 +02:00
Matthias De Smet
c390385cf5 revert wgsmetrics' 2022-05-22 06:44:17 +02:00
Matthias De Smet
d6a0238cd1
Merge branch 'master' into update/picard 2022-05-21 08:34:33 +02:00
Matthias De Smet
a5a6973fcf picard: make reference sequence optional 2022-05-21 08:33:49 +02:00
Ramprasad Neethiraj
635edc0022 fix typo 2022-05-20 17:07:42 +02:00
Ramprasad Neethiraj
2542c9d176 add tests 2022-05-20 16:46:19 +02:00
Mahesh Binzer-Panchal
2926ec0abb Add mash screen 2022-05-20 13:23:11 +00:00
Ramprasad Neethiraj
c70b169f61 create modules 2022-05-20 13:34:54 +02:00
SusiJo
9096be5464 improve readability 2022-05-20 13:29:49 +02:00
SusiJo
bdf222649d remove unnecessary if statement 2022-05-20 13:25:57 +02:00
SusiJo
153c900d0e
refine comment 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-20 13:08:38 +02:00
SusiJo
2e5aa0dbb4
refine comment 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-20 13:08:26 +02:00
SusiJo
3b3921cfa3
refine comment 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-20 13:07:57 +02:00
SusiJo
f392c4bed5 removed params section & added description fasta 2022-05-20 13:05:43 +02:00
SusiJo
129270d7bc adjusted conda env & singularity container 2022-05-20 10:37:46 +02:00
SusiJo
dd2f48810a
Merge branch 'nf-core:master' into cnvkit_bam 2022-05-20 09:14:21 +02:00
SusiJo
5a1297cc7d added optional pdf/png outputs 2022-05-20 09:12:47 +02:00
SusiJo
064712c4ea added cram_bam conversion & tumor_only check 2022-05-20 09:11:45 +02:00
Rike
bb3e64647b Merge remote-tracking branch 'origin/master' into gatk_filter 2022-05-18 15:52:47 +02:00
FriederikeHanssen
44e9cf56fa
Merge branch 'master' into gatk_cnnscore 2022-05-18 15:32:36 +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
James A. Fellows Yates
965fabdd54
Merge branch 'master' into motus_profile 2022-05-18 11:25:48 +01:00
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
Jose Espinosa-Carrasco
3614c19206
Merge branch 'master' into biobambam/bammerge 2022-05-17 15:07:37 +02:00
Nicolas Vannieuwkerke
6342f5b099 added bedtools split 2022-05-17 14:24:32 +02:00
Matthias De Smet
f48790a728
replace regex with fixed extensions 2022-05-17 09:54:06 +02:00
Matthias De Smet
94733a85c0
Update modules/biobambam/bammerge/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-05-17 09:46:19 +02:00
Matthias De Smet
d3ddc2221a
Merge branch 'master' into biobambam/bammerge 2022-05-17 08:26:28 +02:00
Matthias De Smet
6be91ce82d fix optional output detection 2022-05-17 08:20:47 +02:00
Subazini TK
79c2c529fc
Merge branch 'master' into hmtnote 2022-05-17 08:05:47 +02:00
JIANHONG OU
671bacb6df
Merge branch 'master' into motus_profile 2022-05-16 17:34:49 -04:00
Matthias De Smet
d0db186e84
Merge branch 'master' into biobambam/bammerge 2022-05-16 20:52:48 +02:00
Matthias De Smet
a79b9adeee address review comments 2022-05-16 20:51:39 +02:00
Subazini TK
00204fa82b Update main.nf 2022-05-16 15:20:15 +00:00
Subazini TK
a0b46d3f03 Update meta.yml 2022-05-16 15:20:15 +00:00
Subazini TK
eaf81f6835 Update meta.yml 2022-05-16 15:20:15 +00:00
Subazini TK
1c42c97504 Update meta.yml 2022-05-16 15:20:15 +00:00
Subazini TK
8b4c5742c9 Update main.nf 2022-05-16 15:20:15 +00:00
Subazini TK
2a15bc2ac0 Update main.nf 2022-05-16 15:20:15 +00:00
Subazini TK
78dc1af1e6 Update main.nf 2022-05-16 15:20:15 +00:00
sysbiocoder
26f026683b hmtnote 2022-05-16 15:20:15 +00:00
sysbiocoder
31fc8b560f hmtnote 2022-05-16 15:20:15 +00:00
Veit Schwämmle
85345e5f61
Merge branch 'master' into maxquant 2022-05-16 16:06:32 +02:00
Praveen Raj S
df2620cfc7
Merge branch 'master' into process_lable_markdup 2022-05-16 15:53:26 +02:00
Matthias De Smet
98f204fd1f
Update modules/biobambam/bammerge/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-05-16 15:13:54 +02:00
Matthias De Smet
cdbe648400 align 2022-05-16 14:44:32 +02:00
Matthias De Smet
2cca156fed linting 2022-05-16 14:42:34 +02:00
Matthias De Smet
af69ea749d add module: biobambam/bammerge 2022-05-16 14:39:58 +02:00
veitveit
12815af53e ran prettier 2022-05-16 14:30:40 +02:00
Veit Schwämmle
74a1c1400e
Merge branch 'master' into maxquant 2022-05-16 13:26:35 +02:00
Jasmin F
982c9183fa
Merge branch 'master' into antismashlite 2022-05-16 11:42:44 +02:00
Jasmin F
adcfae6cd4
Merge branch 'master' into antismashlite 2022-05-16 10:38:01 +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
Taniguti
ac7fe89a78
Merge branch 'master' into haplocheck 2022-05-13 11:24:10 -03:00
JIANHONG OU
fadb83cf44
Merge branch 'master' into motus_profile 2022-05-13 09:30:20 -04:00
Matthias De Smet
cbc47767f7 add sort option to bowtie2 2022-05-13 15:26:41 +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
4f6264f7c3 Merge branch 'new-module-gatk4/splitintervals' of github.com:nvnieuwk/modules into new-module-gatk4/splitintervals 2022-05-13 13:48:35 +02:00
Nicolas Vannieuwkerke
9d53577282 linting 2022-05-13 13:48:33 +02:00
nvnieuwk
1d4862ba60
Merge branch 'master' into new-module-gatk4/splitintervals 2022-05-13 13:47:20 +02:00