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Author SHA1 Message Date
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
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
3294def3fd
Merge pull request #1722 from SusiJo/deeptools_samtools 
Adjust deeptools/bamcoverage with new mulled container
 2022-06-02 10:50:05 +02:00
SusiJo
a21cfb666e changed container + add cram2bam conversion 2022-06-02 10:38:05 +02:00
nvnieuwk
95e8afe627
Merge pull request #1714 from nvnieuwk/new-module-gatk4/ComposeSTRTableFile 
added gatk4/composestrtablefile
 2022-06-01 09:33:08 +02:00
Nicolas Vannieuwkerke
114a54c8d5 spaces fix 2022-06-01 09:22:09 +02:00
Nicolas Vannieuwkerke
8470f3cb7e linting 2022-06-01 09:20:20 +02:00
Nicolas Vannieuwkerke
d4f3df4677 Updated the test 2022-06-01 09:17:05 +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
James A. Fellows Yates
33af85697b
Merge pull request #1713 from jfy133/fix-filtlong 
Fix filtlong to remove hardcoded output names
 2022-05-31 20:50:21 +02:00
James A. Fellows Yates
615cb0722f
Merge branch 'master' into fix-filtlong 2022-05-31 20:25:16 +02:00
James Fellows Yates
df22cd80df Fix config for tests 2022-05-31 20:07:52 +02:00
FriederikeHanssen
fba7edb652
Merge pull request #1716 from asp8200/get_tbi_files_from_gatk4_mergevcfs 
Get tbi-files from gatk4 mergevcfs
 2022-05-31 17:55:06 +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
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
James Fellows Yates
089f761f0b Actually add the changes 2022-05-31 15:49:57 +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
Anders Sune Pedersen
5513d095f5 Adding tbi-files to the output from GATK4_MERGEVCFS. #1709 2022-05-31 15:37:26 +02:00
nvnieuwk
22a90dbd0f
Merge pull request #1711 from nvnieuwk/add-tbi-to-bcftools-concat 
Added optional input of index files to bcftools/concat
 2022-05-31 15:33:10 +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
94dd8f63df
Merge pull request #1710 from jfy133/fix-filtlong 
Fix filtlong - makes running without shortreads work correctly, and also ensures all tests produce …
 2022-05-31 14:54:54 +02:00
James A. Fellows Yates
0b895871d7
Merge branch 'master' into fix-filtlong 2022-05-31 14:49:44 +02:00
James Fellows Yates
430def06fa Switch from md5sum to string due to conda flakiness 2022-05-31 14:45:41 +02:00
James A. Fellows Yates
667a0bc24c
Merge pull request #1708 from sguizard/bamtools/convert/remove_TODO 
👌 IMPROVE: Remove last TODO
 2022-05-31 13:41:41 +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
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
Jeanette Tångrot
3bb32b2def
Merge pull request #1705 from jtangrot/vsearch_usearch_global 
Vsearch usearch global
 2022-05-30 14:28:01 +02:00
jtangrot
6ae405c5da prettier 2022-05-30 13:35:12 +02:00
jtangrot
6aac5c2c40 Update test 2022-05-30 13:30:27 +02:00
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
jtangrot
2e16c90fce Fix whitespace 2022-05-30 09:57:05 +02:00
jtangrot
5132b004c7 Merge branch 'vsearch_usearch_global' of https://github.com/jtangrot/nf-core_modules into vsearch_usearch_global 2022-05-30 08:55:33 +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
b86d792055
Merge pull request #1703 from drpatelh/star 
Bump container version for STAR to 2.7.10a
 2022-05-27 12:29:59 +01:00
Harshil Patel
ad578cafcc Fix tests 2022-05-27 12:14:10 +01:00