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Author SHA1 Message Date
ljmesi
59d6e6e1dd Add updated md5sums 2022-05-03 09:56:50 +02:00
ljmesi
5503903457 Add compression for output fastq file 2022-05-03 09:46:04 +02:00
Ramprasad Neethiraj
6f787aea71
Merge branch 'master' into adding_stub_to_modules 2022-05-03 09:43:16 +02:00
Lauri Mesilaakso
218400b632
Merge pull request #1600 from Genomic-Medicine-Linkoping/add_handling_of_alternative_fn_suffix_for_metaphlan3 
Add additional handling of fq.gz file name suffix
 2022-05-03 09:50:09 +03:00
Lauri Mesilaakso
77054795fb
Merge branch 'master' into add_handling_of_alternative_fn_suffix_for_metaphlan3 2022-05-03 09:38:51 +03:00
Nicolas Vannieuwkerke
71c5d21374 ran prettier 2022-05-03 08:34:12 +02:00
Nicolas Vannieuwkerke
9127f92ddd Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-05-03 08:29:50 +02:00
Nicolas Vannieuwkerke
9a10e5beb5 Added the missing inputs in meta.yml + correct notation 2022-05-03 08:29:46 +02:00
Matthias De Smet
1687bfcb85
Merge branch 'master' into add-slimfastq 2022-05-03 08:22:49 +02:00
Matthias De Smet
a67c06af81
Merge branch 'master' into vardict-java 2022-05-03 08:22:19 +02:00
Nicolas Vannieuwkerke
d8782d7976 Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-05-03 08:20:13 +02:00
Nicolas Vannieuwkerke
b8a59c2b17 Fixed version annotation 2022-05-03 08:20:10 +02:00
Sateesh Peri
88a9a55c80
Merge pull request #1574 from jvhagey/srst2/srst2 
new module: srst2/srst2
 2022-05-02 20:21:23 -04:00
Jill V. Hagey, PhD
23cfb5dd42
Update test.yml 2022-05-02 18:38:48 -04:00
Jill V. Hagey, PhD
db9681029c
Update test.yml 2022-05-02 18:27:01 -04:00
Jill V. Hagey, PhD
7b0d6f96fd
Update test.yml 2022-05-02 18:20:54 -04:00
Jill V. Hagey, PhD
e5d7c80bb5
Update test.yml 2022-05-02 18:13:14 -04:00
Moritz E. Beber
16aa3915e3 feat: add module for slimfastq 2022-05-02 23:16:59 +02:00
Carpanzano
d2e1408b0f updated content for html file in test yml 2022-05-02 18:44:05 +02:00
carpanz
e8b2445878 updated file location in test yml 2022-05-02 18:43:20 +02:00
Carpanzano
1deb789502 synced withName ext.args with process name 2022-05-02 18:39:45 +02:00
Carpanzano
5136ed29c4 removed include and changed process name due to expected folder name before tokenize 2022-05-02 18:38:59 +02:00
Ramprasad Neethiraj
3194729f82
Merge branch 'master' into adding_stub_to_modules 2022-05-02 18:31:55 +02:00
Jill V. Hagey, PhD
99a8711997
Update tests/modules/srst2/srst2/test.yml 
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
 2022-05-02 12:26:56 -04:00
JIANHONG OU
5735f515f8 fix a typo in version export. 2022-05-02 12:25:48 -04:00
Carpanzano
32b8f3f612 adding contain for html output in test yml 2022-05-02 18:21:26 +02:00
carpanz
6e83196634 updating test yml after removing kronadb from test 2022-05-02 18:20:36 +02:00
Carpanzano
b0a2d36ec1 removing kronadb module from testing ktimporttaxonomy test - NB: temporarily using test db while testdb is added to test-datasets 2022-05-02 18:16:08 +02:00
Sateesh Peri
c56b371713
Merge branch 'master' into srst2/srst2 2022-05-02 12:13:11 -04:00
Carpanzano
c07ae8c483 fixed lint in ktimporttaxonomy 2022-05-02 17:47:45 +02:00
Simone Carpanzano
3d9c8a6bb1
Merge branch 'master' into firstbranch 2022-05-02 17:43:33 +02:00
Carpanzano
c9ab26ba8e synced name of report as in test config 2022-05-02 17:41:55 +02:00
Carpanzano
76a0e3ef04 updated config kraken report name 2022-05-02 17:40:50 +02:00
jvhagey
cd45dc1550 linting test.yml 2022-05-02 11:38:39 -04:00
Jasmin F
f70cfbe1d7
Merge pull request #1581 from jasmezz/antismash_db_output 
Antismash db output
 2022-05-02 17:37:01 +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
Jasmin F
8db0b754c0
Fix commented-out command 2022-05-02 16:56:39 +02:00
Carpanzano
700d6ab3f1 errore TDOWNLOAD 2022-05-02 16:55:18 +02:00
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