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Author SHA1 Message Date
jasmezz
6a9f2077cf Fix unbound variable crash 2022-05-02 16:41:59 +02:00
Carpanzano
80f107515e update nextflow.config withName 2022-05-02 16:22:22 +02:00
Carpanzano
42310cbce2 updated config to reflect names in test workflow 2022-05-02 16:14:38 +02:00
Carpanzano
38d9d81aaf update code 2022-05-02 16:10:57 +02:00
Lucpen
50cc136a78
Update tests/modules/gatk4/mutect2/main.nf 
fix spelling mistake

Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
 2022-05-02 15:14:05 +02:00
Lucpen
62c6123ec4 fix gatk4_mutect2 test by changing main.nf 2022-05-02 15:11:57 +02:00
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
jasmezz
0fc352188b Fix conda antismash path 2022-05-02 14:40:35 +02:00
JIANHONG OU
0f24e4dcff add input database and intermediate bam file. 2022-05-02 08:37:12 -04:00
Jasmin F
5cd517e759
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-02 14:31:40 +02:00
Lucpen
dfabf960dc
Merge branch 'master' into adding_stub_to_modules 2022-05-02 14:20:03 +02:00
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
ljmesi
ed4dd1a928 Add additional handling of fq.gz file name suffix 2022-05-02 14:16:12 +02:00
Lucpen
da82e06354 fix gatk4_mutect2 test 2022-05-02 14:16:07 +02:00
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
Lucpen
3a4e415fe2 chores adding dummy files for stubs 2022-05-02 13:30:18 +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
Lucpen
de40c1bf54 chore removing file from test 2022-05-02 13:15:01 +02:00
Lucpen
f231291e77 fix gatk4_reversam test 2022-05-02 12:58:12 +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
Lucpen
08d5acbeb6 feat added tests for stubs 2022-05-02 11:59:08 +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
Lucpen
8a5bcbc325 fix the stub of gatk4_revertsam 2022-05-02 11:06:08 +02:00
Matthias De Smet
bf416f2307
Merge branch 'master' into vardict-java 2022-05-02 10:43:47 +02:00
Lucpen
6b64f9cb6c feat added stub to modules 2022-05-02 10:34:14 +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
Ramprasad Neethiraj
9a9f3e97de fix md5sums 2022-05-01 21:51:40 +02:00
Ramprasad Neethiraj
d2004a2b76 update cnvpytor 2022-05-01 21:14:01 +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
Carpanzano
41fd2d1557 modifiche 2022-04-29 17:52:12 +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