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Author SHA1 Message Date
Matthias De Smet
a9e8dbbdec
Merge pull request #1535 from matthdsm/tool/bamtools-split 2022-04-29 18:43:44 +02:00
Harshil Patel
4df985a065
Merge branch 'master' into tool/bamtools-split 2022-04-29 16:38:59 +01:00
Edmund Miller
0d8acda00c
Use issue forms 2022-04-29 14:35:29 +00:00
Edmund Miller
a8a4d76a65 chore: Add container version 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-04-29 14:34:20 +00:00
Edmund Miller
fb02d6e85f chore: add OS version to bug report 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-04-29 14:34:20 +00:00
Edmund Miller
8bee7d4748 chore: Add image tag to bug report 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-04-29 14:34:20 +00:00
Edmund Miller
ef0483586a chore: Use forms for feature request 2022-04-29 14:34:20 +00:00
Edmund Miller
816803dbe9 chore: Add checkboxes for bug report 2022-04-29 14:34:20 +00:00
Edmund Miller
2da712f6f3 chore: Use forms for new modules 2022-04-29 14:34:20 +00:00
Edmund Miller
cb29ae2187 chore: Use forms for bug report 2022-04-29 14:34:20 +00:00
Matthias De Smet
86484f3361
Merge pull request #1534 from matthdsm/tool/elprep-merge 
Tool/elprep merge
 2022-04-29 15:18:45 +02:00
James A. Fellows Yates
23c42e9b76
Merge branch 'master' into tool/elprep-merge 2022-04-29 15:11:09 +02:00
James A. Fellows Yates
fa8edd917f
Merge pull request #1587 from jfy133/diamond-update 
Update DIAMOND/blast* to support all output formats
 2022-04-29 15:08:18 +02:00
Matthias De Smet
9d0f03d96a
Update modules/elprep/merge/main.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-29 15:07:09 +02:00
Matthias De Smet
7de207f93f
Merge branch 'master' into diamond-update 2022-04-29 15:02:54 +02:00
Matthias De Smet
bdbf629d93
Merge branch 'master' into tool/bamtools-split 2022-04-29 14:33:28 +02:00
Matthias De Smet
edadc9d216
Merge branch 'master' into tool/elprep-merge 2022-04-29 14:32:12 +02:00
Matthias De Smet
0ec3dea37f
Merge pull request #1541 from matthdsm/subwf/bam_qc 
New subworkflow:  bam_qc_picard
 2022-04-29 14:31:38 +02:00
Matthias De Smet
7e391c3a3b
Update subworkflows/nf-core/bam_qc_picard/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-29 14:26:06 +02:00
Matthias De Smet
343c0ebe20
Update subworkflows/nf-core/bam_qc_picard/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-29 14:26:00 +02:00
Matthias De Smet
20e3767657
Update subworkflows/nf-core/bam_qc_picard/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-29 14:24:25 +02:00
Matthias De Smet
71ccf0e207
Update subworkflows/nf-core/bam_qc_picard/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-29 14:24:19 +02:00
Matthias De Smet
73600b0339
Update subworkflows/nf-core/bam_qc_picard/main.nf 
Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>
 2022-04-29 14:20:15 +02:00
Matthias De Smet
3997d28a77
Merge branch 'master' into subwf/bam_qc 2022-04-29 11:39:18 +02:00
Matthias De Smet
c55032d10e
Merge pull request #1584 from matthdsm/bump/picard 
bump picard version across the board
 2022-04-29 11:38:21 +02:00
Matthias De Smet
771d5a19f1 fix reference arg 2022-04-29 11:12:24 +02:00
Matthias De Smet
20ebb89ff9 update to long args 2022-04-29 10:52:40 +02:00
James A. Fellows Yates
983d61763d
Merge branch 'master' into diamond-update 2022-04-29 10:28:38 +02:00
James Fellows Yates
7df2fae746 Clean up test data 2022-04-29 10:26:38 +02:00
James Fellows Yates
42564565b9 Update diamond/blastx diamond/blastp to support all possible output formats 2022-04-29 10:26:17 +02:00
Matthias De Smet
b2e4342105 fix args in nextflow.config 2022-04-29 10:21:22 +02:00
Matthias De Smet
bda132191d fix args in nextflow.config 2022-04-29 10:13:39 +02:00
CMGG ICT Team
0e01d703ea remove version md5sum from fixmateinformation 2022-04-29 10:12:52 +02:00
Matthias De Smet
e263f267a7
Merge branch 'master' into bump/picard 2022-04-29 09:48:15 +02:00
Lauri Mesilaakso
1a5a9e7b40
Fix typo (#1586) 2022-04-29 09:37:23 +02:00
Matthias De Smet
ec10f98d55
picard CollectWgsMetrics: update to new cli args (#1578) 
* update to new cli args

* remove bam index from tuple, not needed by program

* bump picard version

Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
 2022-04-29 09:32:32 +02:00
James A. Fellows Yates
4e73a9e9c5
Merge branch 'nf-core:master' into master 2022-04-29 09:10:07 +02:00
Matthias De Smet
b72ec05d69 drop md5sum from versions.yml 2022-04-29 08:19:42 +02:00
Matthias De Smet
00467ac64a update command line syntax for all tools 2022-04-29 07:57:11 +02:00
Matthias De Smet
6ca6de91f8 bump picard version across the board 2022-04-29 07:47:24 +02:00
Matthias De Smet
da94b776ef
Merge branch 'master' into subwf/bam_qc 2022-04-28 22:12:48 +02:00
Matthias De Smet
4d913d337d
Merge branch 'master' into tool/bamtools-split 2022-04-28 21:17:46 +02:00
Matthias De Smet
a7ed1477ee
Merge branch 'master' into tool/elprep-merge 2022-04-28 21:14:30 +02:00
Jill V. Hagey, PhD
218769d7df
Update modules/srst2/srst2/main.nf 
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
 2022-04-28 14:41:37 -04:00
Jill V. Hagey, PhD
842ae3982b
Update meta.yml 2022-04-28 14:39:02 -04:00
Jill V. Hagey, PhD
9e7e10305b
Update modules/srst2/srst2/meta.yml 
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
 2022-04-28 14:02:28 -04:00
Sateesh Peri
f5c4aecde5
Merge branch 'master' into srst2/srst2 2022-04-28 13:49:51 -04:00
Jill V. Hagey, PhD
e29a69077d
add doi 2022-04-28 12:30:04 -04:00
Jill V. Hagey, PhD
5be6afd6b1
changed container 2022-04-28 12:29:39 -04:00
Robert A. Petit III
4b6ee6fc14
Merge branch 'master' into rp3-add-shigatyper 2022-04-28 09:51:36 -06:00