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Author SHA1 Message Date
Chris Cheshire
40e6bd9dc1 bowtie2|fix tags error 2022-05-03 12:07:04 +01:00
Chris Cheshire
0f1ee7e50d bowtie2|test fixes 2022-05-03 12:04:51 +01:00
Chris Cheshire
61f68913fe
Merge branch 'master' into expected_error_fix 2022-05-03 11:49:35 +01:00
Chris Cheshire
768073be63 bowtie2|Added support for large indexes 2022-05-03 11:46:19 +01:00
James A. Fellows Yates
b61cdc7355
Merge pull request #1570 from nvnieuwk/vardict-java 
new_module:vardict-java
 2022-05-03 10:26:41 +02:00
nvnieuwk
f85787b19e
Merge branch 'master' into vardict-java 2022-05-03 10:17:04 +02:00
nvnieuwk
8187641280
Update modules/vardictjava/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-03 10:16:45 +02:00
nvnieuwk
11c6faf433
Update modules/vardictjava/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-03 10:16:36 +02:00
nvnieuwk
01085b3e09
Update modules/vardictjava/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-03 10:16:30 +02:00
nvnieuwk
1609dfc96d
Update modules/vardictjava/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-03 10:16:20 +02:00
nvnieuwk
3cdbdf50fc
Update modules/vardictjava/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-03 10:16:14 +02:00
nvnieuwk
2dff193b54
Update modules/vardictjava/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-03 10:15:59 +02:00
nvnieuwk
7c89af359c
Update modules/vardictjava/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-03 10:15:51 +02:00
Nicolas Vannieuwkerke
49ba3adbde Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-05-03 10:15:33 +02:00
Nicolas Vannieuwkerke
d33253513f put the version on top of the file 2022-05-03 10:15:30 +02:00
Lucpen
3891eca3c3
Merge pull request #1596 from nf-core/adding_stub_to_modules 
feat added stub to modules gatk4_mergebamalignment_mutect2_revertsam_samtofastq, samtools_view
 2022-05-03 10:13:25 +02:00
nvnieuwk
278d41b6bf
Merge branch 'master' into vardict-java 2022-05-03 09:59:05 +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
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
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
Sateesh Peri
c56b371713
Merge branch 'master' into srst2/srst2 2022-05-02 12:13:11 -04:00
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
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
jasmezz
6a9f2077cf Fix unbound variable crash 2022-05-02 16:41:59 +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
jasmezz
0fc352188b Fix conda antismash path 2022-05-02 14:40:35 +02:00
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
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