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815 commits

Author SHA1 Message Date
JIANHONG OU
e9c82a5f48
Update modules/motus/downloaddb/meta.yml 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-04 15:29:06 -04:00
James A. Fellows Yates
35b5ba673f
Merge branch 'master' into motus_downloaddb 2022-05-04 20:58:08 +02:00
James A. Fellows Yates
ec5bada3fc
Update modules/motus/downloaddb/meta.yml 2022-05-04 20:55:16 +02:00
Lauri Mesilaakso
e757966566
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 18:41:36 +03:00
Carpanzano
a6086f549d recovered process name 2022-05-04 17:28:24 +02:00
Nicolas Vannieuwkerke
3c07602443 Added the version.yml 2022-05-04 16:51:09 +02:00
Carpanzano
8b1711d8a1 recovering old module name 2022-05-04 16:38:10 +02:00
Simone Carpanzano
162f8edf54
Merge branch 'master' into firstbranch 2022-05-04 16:35:25 +02:00
Carpanzano
6b8ca501ed fixing suggestions from PR 2022-05-04 16:34:52 +02:00
Nicolas Vannieuwkerke
f875aec46b Split the module into two parts 2022-05-04 15:29:48 +02:00
Mahesh Binzer-Panchal
5986a3efbf
Merge branch 'master' into busco 2022-05-04 15:09:54 +02:00
Nicolas Vannieuwkerke
505ab03803 fixed a description 2022-05-04 14:14:53 +02:00
Nicolas Vannieuwkerke
177a7e49f2 Fixed a linting issue 2022-05-04 14:06:42 +02:00
Nicolas Vannieuwkerke
000b8ee2e0 Merge branch 'new-module-hap.py' of github.com:nvnieuwk/modules into new-module-hap.py 2022-05-04 14:05:23 +02:00
Nicolas Vannieuwkerke
065a5d6a7f Fixed a linting issue 2022-05-04 14:05:21 +02:00
nvnieuwk
c9808cb97f
Merge branch 'master' into new-module-hap.py 2022-05-04 14:01:02 +02:00
Nicolas Vannieuwkerke
37338ecee3 Finished the module 2022-05-04 14:00:02 +02:00
Ramprasad Neethiraj
6541e151bc
Merge branch 'master' into feat/update_cnvpytor 2022-05-04 13:54:46 +02:00
Mahesh Binzer-Panchal
73a8df9522 Fix no genes found test and update test.yml 2022-05-04 11:52:42 +00:00
Nicolas Vannieuwkerke
c517ce9b4d Added the module and some simple testing 2022-05-04 13:42:12 +02:00
Mahesh Binzer-Panchal
8df20218bf Add more tests and capture summaries 
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
 2022-05-04 09:22:43 +00:00
Mahesh Binzer-Panchal
3bb0711b06
Merge branch 'master' into busco 2022-05-04 09:15:46 +02:00
Lauri Mesilaakso
530b5ac661
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 09:53:46 +03:00
Chris Cheshire
79e64cdd1f
Merge branch 'master' into expected_error_fix 2022-05-03 22:21:28 +01:00
JIANHONG OU
dc59ad0bf5 fix the version issue. 2022-05-03 12:27:39 -04:00
Jill V. Hagey, PhD
f02cd618b8
Update meta.yml 2022-05-03 10:09:19 -04:00
Lauri Mesilaakso
12f79c2101
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 17:03:02 +03:00
Mahesh Binzer-Panchal
1c54c0b1ae
Apply suggestions from code review 
Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
 2022-05-03 16:02:11 +02:00
Matthieu Muffato
6351ec745e
Update contributor list 2022-05-03 14:56:27 +01:00
Matthieu Muffato
4be754b008
It's a file, not a directory 2022-05-03 14:53:17 +01:00
Mahesh Binzer-Panchal
636abad8f1
Merge branch 'master' into busco 2022-05-03 15:38:25 +02:00
Nicolas Vannieuwkerke
96d4a31cc1 Moved the BED file to the main tuple 2022-05-03 15:31:05 +02:00
Mahesh Binzer-Panchal
5f4781adaa
Merge branch 'master' into busco 2022-05-03 15:27:10 +02:00
Mahesh Binzer-Panchal
57db28386e Support batch fasta analysis 2022-05-03 13:26:49 +00:00
ljmesi
034352dbbf Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq 2022-05-03 15:18:12 +02:00
ljmesi
5510ea39fe Test --no-name to solve inconsistent checksums 2022-05-03 15:18:09 +02:00
Ramprasad Neethiraj
26311aba2a fix minor errors 2022-05-03 15:04:37 +02:00
Ramprasad Neethiraj
be085c0173 Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor 2022-05-03 14:55:42 +02:00
Ramprasad Neethiraj
19cfb4e951 update meta files 2022-05-03 14:53:56 +02:00
Ramprasad Neethiraj
3efa931bf6 view 2022-05-03 14:26:46 +02:00
Ramprasad Neethiraj
829c15c98b partition 2022-05-03 14:26:34 +02:00
Ramprasad Neethiraj
7cc47f6ba6 importrd 2022-05-03 14:25:20 +02:00
Ramprasad Neethiraj
07e026054a histogram 2022-05-03 14:24:54 +02:00
Ramprasad Neethiraj
2990dc8357 callcnv module 2022-05-03 14:20:05 +02:00
Lauri Mesilaakso
a65e76e3dd
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 14:30:54 +03:00
Chris Cheshire
6f35537d40
Merge branch 'master' into expected_error_fix 2022-05-03 12:21:51 +01:00
Chris Cheshire
829183ee84
Merge branch 'master' into rp3-add-shigatyper 2022-05-03 12:16:54 +01:00
Chris Cheshire
6015478b72
Merge branch 'master' into add-slimfastq 2022-05-03 12:11:19 +01:00
Chris Cheshire
d7fb969a74
Merge branch 'master' into rp3-add-shigatyper 2022-05-03 12:10:23 +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
Mahesh Binzer-Panchal
012f085378 Prettier 2022-05-03 09:19:39 +00:00
Mahesh Binzer-Panchal
9eff38ff94 Update meta.yml 2022-05-03 09:15:45 +00:00
Mahesh Binzer-Panchal
ddbe6e8f40
Merge branch 'master' into busco 2022-05-03 10:48:03 +02:00
Mahesh Binzer-Panchal
9a72548ee1 Update busco module 2022-05-03 08:42:56 +00:00
Lauri Mesilaakso
6367c6a1ad
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 11:41:25 +03:00
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
Lauri Mesilaakso
773e6f8e93
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 11:13:55 +03:00
nvnieuwk
278d41b6bf
Merge branch 'master' into vardict-java 2022-05-03 09:59:05 +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
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
Moritz E. Beber
16aa3915e3 feat: add module for slimfastq 2022-05-02 23:16:59 +02:00
Ramprasad Neethiraj
3194729f82
Merge branch 'master' into adding_stub_to_modules 2022-05-02 18:31:55 +02:00
JIANHONG OU
5735f515f8 fix a typo in version export. 2022-05-02 12:25:48 -04:00
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
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
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
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
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
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
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
Ramprasad Neethiraj
d2004a2b76 update cnvpytor 2022-05-01 21:14:01 +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
Harshil Patel
4df985a065
Merge branch 'master' into tool/bamtools-split 2022-04-29 16:38:59 +01:00
James A. Fellows Yates
23c42e9b76
Merge branch 'master' into tool/elprep-merge 2022-04-29 15:11:09 +02:00
Matthias De Smet
9d0f03d96a
Update modules/elprep/merge/main.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-29 15:07:09 +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
Matthias De Smet
771d5a19f1 fix reference arg 2022-04-29 11:12:24 +02:00
Matthias De Smet
20ebb89ff9 update to long args 2022-04-29 10:52:40 +02:00
James A. Fellows Yates
983d61763d
Merge branch 'master' into diamond-update 2022-04-29 10:28:38 +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
e263f267a7
Merge branch 'master' into bump/picard 2022-04-29 09:48:15 +02:00
Lauri Mesilaakso
1a5a9e7b40
Fix typo (#1586) 2022-04-29 09:37:23 +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
00467ac64a update command line syntax for all tools 2022-04-29 07:57:11 +02:00
Matthias De Smet
6ca6de91f8 bump picard version across the board 2022-04-29 07:47:24 +02:00
Simone Carpanzano
2efa5a09ab
Update main.nf 
$args line 28
 2022-04-29 00:00:13 +02:00
Matthias De Smet
4d913d337d
Merge branch 'master' into tool/bamtools-split 2022-04-28 21:17:46 +02:00
Matthias De Smet
a7ed1477ee
Merge branch 'master' into tool/elprep-merge 2022-04-28 21:14:30 +02:00
Jill V. Hagey, PhD
218769d7df
Update modules/srst2/srst2/main.nf 
Co-authored-by: Edmund Miller <edmund.a.miller@gmail.com>
 2022-04-28 14:41:37 -04:00
Jill V. Hagey, PhD
842ae3982b
Update meta.yml 2022-04-28 14:39:02 -04:00
Jill V. Hagey, PhD
9e7e10305b
Update modules/srst2/srst2/meta.yml 
Co-authored-by: Sateesh Peri <33637490+sateeshperi@users.noreply.github.com>
 2022-04-28 14:02:28 -04:00
Sateesh Peri
f5c4aecde5
Merge branch 'master' into srst2/srst2 2022-04-28 13:49:51 -04:00
Jill V. Hagey, PhD
e29a69077d
add doi 2022-04-28 12:30:04 -04:00
Jill V. Hagey, PhD
5be6afd6b1
changed container 2022-04-28 12:29:39 -04:00
Robert A. Petit III
4b6ee6fc14
Merge branch 'master' into rp3-add-shigatyper 2022-04-28 09:51:36 -06:00
Jasmin F
c740853874
Antismash db output patch 1 (#3) 
* Update main.nf

* Update meta.yml

* Update test.yml
 2022-04-28 16:42:44 +02:00
Nicolas Vannieuwkerke
4b04ca22dd Variable name change for var2vcf conversion arguments 2022-04-28 16:38:49 +02:00
Nicolas Vannieuwkerke
d626a1dcd3 Removed a whitespace in meta.yml... 2022-04-28 15:41:43 +02:00
nvnieuwk
a6397fac8f
Merge branch 'master' into vardict-java 2022-04-28 15:34:46 +02:00
Nicolas Vannieuwkerke
bdff37c3d7 Added the statistical tests and conversion to vcf 2022-04-28 15:33:27 +02:00
Nicolas Vannieuwkerke
6678ad4426 Added a header to the VCF 2022-04-28 14:54:20 +02:00
Praveen Raj S
b3e9b88e80
csi output in TABIX (#1579) 
* Added: csi output to TABIX

* Added: tests for csi

* Fix tiddit/sv (#1580)

* Fix fasta ref option for TIDDIT_SV

* Add md5sum's to tiddit/sv tests

Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>

* Fix: prettier issues

Co-authored-by: Daniel Cooke <daniel.cooke@invitae.com>
Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
 2022-04-28 14:41:01 +02:00
nvnieuwk
c9404ed266
Merge branch 'master' into vardict-java 2022-04-28 14:30:19 +02:00
Nicolas Vannieuwkerke
40e6e5273d fix for a linting issue 2022-04-28 14:30:04 +02:00
Nicolas Vannieuwkerke
c6ea41948d Merge branch 'vardict-java' of github.com:nvnieuwk/modules into vardict-java 2022-04-28 14:29:39 +02:00
Nicolas Vannieuwkerke
bf18604471 fix for a linting issue 2022-04-28 14:29:37 +02:00
JIANHONG OU
cdefbec669
add kimporttext module (#1560) 
* add kimporttext module

* fix the Prettier error.

* fix the Prettier error.

* fix the test.yml

* fix the test.yml

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update modules/krona/ktimporttext/meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* update the test files;
simplify the main script of krona/ktimporttext.

* update the test file url for krona ktimporttext

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-04-28 08:16:26 -04:00
JIANHONG OU
24fb7c89aa
Update modules/motus/downloaddb/main.nf 
Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
 2022-04-28 08:14:30 -04:00
Matthias De Smet
c7806e7bef
Merge branch 'master' into vardict-java 2022-04-28 14:12:07 +02:00
Nicolas Vannieuwkerke
8c98a78d2a Fixed the issue with the BED file 2022-04-28 14:07:55 +02:00
Daniel Cooke
57cb730e78
Fix tiddit/sv (#1580) 
* Fix fasta ref option for TIDDIT_SV

* Add md5sum's to tiddit/sv tests

Co-authored-by: Daniel Cooke <dcooke@well.ox.ac.uk>
 2022-04-28 14:06:38 +02:00