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2498 commits 30 branches 0 tags 142 MiB
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687 commits

Author SHA1 Message Date
jvhagey
cd45dc1550 linting test.yml 2022-05-02 11:38:39 -04:00
Jasmin F
883b95bed6
Merge branch 'nf-core:master' into antismashlite 2022-05-02 17:31:43 +02:00
jasmezz
4a4de550b8 Simplify/reduce container mount volumes 2022-05-02 17:30:46 +02:00
jvhagey
24dc2d2113 added tests 2022-05-02 11:30:19 -04:00
Carpanzano
1188264fa2 finished test yml file 2022-05-02 17:25:58 +02:00
carpanz
028dc3cb87 updated test yml file 2022-05-02 17:24:55 +02:00
Carpanzano
3cebcbfc0a remove taxonomy not used in place of db 2022-05-02 17:13:58 +02:00
Carpanzano
2e4c200a26 remove new line between includes 2022-05-02 17:13:20 +02:00
Jasmin F
235944f797
Merge branch 'master' into antismash_db_output 2022-05-02 17:11:51 +02:00
Carpanzano
700d6ab3f1 errore TDOWNLOAD 2022-05-02 16:55:18 +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
JIANHONG OU
b14f30936e
Merge branch 'nf-core:master' into motus_downloaddb 2022-05-02 08:42:09 -04:00
Lucpen
dfabf960dc
Merge branch 'master' into adding_stub_to_modules 2022-05-02 14:20:03 +02:00
JIANHONG OU
3f07761da5 remove the output check for the versions.yml. 2022-05-02 08:19:13 -04:00
Lucpen
da82e06354 fix gatk4_mutect2 test 2022-05-02 14:16:07 +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
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
James Fellows Yates
6986975bc0 Fix output channels allow BLAST table customisation 2022-05-02 11:39:07 +02:00
Matthias De Smet
bf416f2307
Merge branch 'master' into vardict-java 2022-05-02 10:43:47 +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
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
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
Carpanzano
6bf0a407f6 modifiche nextflow.config 2022-04-29 15:51:27 +02:00
Simone Carpanzano
d9d0eb393b
Update nextflow.config 2022-04-29 15:39:50 +02:00
Carpanzano
20787514d9 modifiche per il test 2022-04-29 15:11:21 +02:00
James A. Fellows Yates
23c42e9b76
Merge branch 'master' into tool/elprep-merge 2022-04-29 15:11:09 +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
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
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
Matthias De Smet
b72ec05d69 drop md5sum from versions.yml 2022-04-29 08:19:42 +02:00
Matthias De Smet
4d913d337d
Merge branch 'master' into tool/bamtools-split 2022-04-28 21:17:46 +02:00