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Author SHA1 Message Date
Lauri Mesilaakso
773e6f8e93
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 11:13:55 +03:00
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
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
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
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
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
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