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Author SHA1 Message Date
JIANHONG OU
250d64dfde fix the typo of motus_downloadb. 2022-05-02 08:52:54 -04:00
JIANHONG OU
b14f30936e
Merge branch 'nf-core:master' into motus_downloaddb 2022-05-02 08:42:09 -04:00
JIANHONG OU
31dd31079d update teh versions.yml 2022-05-02 08:41:41 -04:00
JIANHONG OU
f1e4591468 Merge branch 'motus_downloaddb' of github.com:jianhong/modules into motus_downloaddb 2022-05-02 08:19:16 -04:00
JIANHONG OU
3f07761da5 remove the output check for the versions.yml. 2022-05-02 08:19:13 -04:00
James A. Fellows Yates
92efb83ec8
Merge pull request #1595 from jfy133/diamond-update 
Standardise DIAMOND output channels and md5sum
 2022-05-02 13:43:56 +02:00
James A. Fellows Yates
f1c2f624eb
Update tests/modules/diamond/blastx/main.nf 
Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
 2022-05-02 13:17:22 +02:00
James A. Fellows Yates
575258332a
Merge branch 'master' into diamond-update 2022-05-02 12:41:37 +02:00
James Fellows Yates
bd3bfe0817 Add warn of default being used 2022-05-02 12:41:24 +02:00
James Fellows Yates
67b074382e Fix tests 2022-05-02 12:29:00 +02:00
James Fellows Yates
58e5c6aece Make variables consistent 2022-05-02 11:55:43 +02:00
Maxime U. Garcia
0b01607659
Merge pull request #1597 from praveenraj2018/optional_bai_MarkDup 
Changed BAI as optional output
 2022-05-02 11:46:19 +02:00
James Fellows Yates
375b706a4f Merge branch 'diamond-update' of github.com:jfy133/nf-core-modules into diamond-update 2022-05-02 11:39:09 +02:00
James Fellows Yates
6986975bc0 Fix output channels allow BLAST table customisation 2022-05-02 11:39:07 +02:00
Praveen
0511e7fbbf Changed BAI as optional output to handle large genome 2022-05-02 11:35:15 +02:00
James A. Fellows Yates
ebd3cebee5
Merge branch 'master' into diamond-update 2022-05-02 09:37:46 +02:00
James Fellows Yates
996385fb0f Remove MD5sumfor DIAMOND DAA file due to occasioanlly variability 2022-05-02 09:36:34 +02:00
Harshil Patel
76ac37c529
Merge pull request #1592 from jfy133/diamond-update 
Bump DIAMOND modules to 2.0.15
 2022-04-29 20:11:26 +01:00
James Fellows Yates
44ed38beb8 Merge branch 'diamond-update' of github.com:jfy133/nf-core-modules into diamond-update 2022-04-29 21:06:09 +02:00
James Fellows Yates
39530b5ca7 Bump DIAMOND version to 2.0.15 2022-04-29 21:05:12 +02:00
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