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2487 commits 30 branches 0 tags 142 MiB
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679 commits

Author SHA1 Message Date
Nicolas Vannieuwkerke
84b354ab6a Added the rtgtools/vcfeval module 2022-05-06 14:23:40 +02:00
Matthias De Smet
3930ba227b merge snapaligner modes into one 2022-05-06 14:10:44 +02:00
Mahesh Binzer-Panchal
a9f23bb477
Merge branch 'master' into busco 2022-05-06 13:49:01 +02:00
Mahesh Binzer-Panchal
35c5828f43 Add --auto-lineage option and remove single_end 
Co-authored-by: Jill V. Hagey, PhD <jvhagey@gmail.com>
 2022-05-06 11:48:21 +00:00
Jose Espinosa-Carrasco
035655e35d
Merge branch 'master' into modules/md5sum 2022-05-06 12:34:14 +02:00
Mahesh Binzer-Panchal
c19e7da59d
Apply suggestions from code review 
Remove versions md5sum

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-06 10:55:48 +02:00
Matthias De Smet
09e729ad41 added sha256sum 2022-05-06 10:28:14 +02:00
Mahesh Binzer-Panchal
d83281eac9
Merge branch 'master' into kat_hist 2022-05-06 10:02:44 +02:00
Mahesh Binzer-Panchal
9194fb845e Add module kat hist 2022-05-06 07:54:10 +00:00
Matthias De Smet
853b623969 new module: md5sum 2022-05-06 09:20:40 +02:00
Ramprasad Neethiraj
db56d80060 Merge branch 'master' of https://github.com/nf-core/modules into feat/update_cnvpytor 2022-05-06 00:10:28 +02:00
Ramprasad Neethiraj
e4e4f8090c combine multiple pytor 2022-05-05 23:59:12 +02:00
Sateesh Peri
faf45edc5e
Merge branch 'master' into busco 2022-05-05 12:48:39 -04:00
Ramprasad Neethiraj
db2acba71b
Merge branch 'master' into feat/update_cnvpytor 2022-05-05 17:31:10 +02:00
Sateesh Peri
3414d3aba3
Merge branch 'master' into busco 2022-05-05 10:08:55 -04:00
JIANHONG OU
a8bc386ea3
Merge branch 'master' into motus_downloaddb 2022-05-05 09:36:25 -04:00
JIANHONG OU
566c11dacc
Merge branch 'master' into motus_downloaddb 2022-05-05 08:28:10 -04:00
Francesco L
97f318eea6
Merge branch 'master' into firstbranch 2022-05-05 14:25:00 +02:00
Carpanzano
a700a9c15e Merge branch 'firstbranch' of github.com:carpanz/modules into firstbranch 2022-05-05 13:52:45 +02:00
Carpanzano
9083d3bb3d integrating suggestions from PR comments, including recovery of tests for kronadb and more detailed explanation of input database in yml file 2022-05-05 13:51:41 +02:00
MaxUlysse
40dd662fd2 update ensemblvep and snpeff modules 2022-05-05 12:57:14 +02:00
James A. Fellows Yates
e60c6f9bfd
Merge branch 'master' into firstbranch 2022-05-05 10:57:27 +02:00
Mahesh Binzer-Panchal
58ea709f7f
Merge branch 'master' into busco 2022-05-05 09:34:14 +02:00
ljmesi
888e122f05 Merge branch 'add_compression_to_bam2fq' of https://github.com/Genomic-Medicine-Linkoping/modules into add_compression_to_bam2fq 2022-05-05 08:32:48 +02:00
ljmesi
be8ce6de2a Remove variable md5sum from the tests 2022-05-05 08:32:45 +02:00
James A. Fellows Yates
35b5ba673f
Merge branch 'master' into motus_downloaddb 2022-05-04 20:58:08 +02:00
Lauri Mesilaakso
e757966566
Merge branch 'master' into add_compression_to_bam2fq 2022-05-04 18:41:36 +03:00
Carpanzano
38faf040ec missing change in ext.args config 2022-05-04 16:54:15 +02:00
Nicolas Vannieuwkerke
3c07602443 Added the version.yml 2022-05-04 16:51:09 +02:00
Carpanzano
e7b92a7616 fixing md5sum changes 2022-05-04 16:43:22 +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
3c66138672 Linting issue + removed the contains lines 2022-05-04 14:49:17 +02:00
Nicolas Vannieuwkerke
5889d6c923 Another possible fix for the pytest issues 2022-05-04 14:46:15 +02:00
Nicolas Vannieuwkerke
583ea13800 Another try to fix the pytest issues 2022-05-04 14:22:55 +02:00
Nicolas Vannieuwkerke
17dbd2bb82 Linting issue fixed 2022-05-04 14:18:56 +02:00
Nicolas Vannieuwkerke
c1393bf999 Possible fix for the pytest errors? 2022-05-04 14:14:01 +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
Mahesh Binzer-Panchal
f65abe1e9a Prettier 2022-05-04 11:54:51 +00:00
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
Lauri Mesilaakso
12f79c2101
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 17:03:02 +03:00
ljmesi
a39fa4e003 Fix checksum for one file 2022-05-03 15:47:49 +02:00
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
46e5752b82 update tests 2022-05-03 14:32:45 +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
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
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
Lauri Mesilaakso
773e6f8e93
Merge branch 'master' into add_compression_to_bam2fq 2022-05-03 11:13:55 +03:00
ljmesi
59d6e6e1dd Add updated md5sums 2022-05-03 09:56:50 +02:00
Ramprasad Neethiraj
6f787aea71
Merge branch 'master' into adding_stub_to_modules 2022-05-03 09:43:16 +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
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
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
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
jvhagey
cd45dc1550 linting test.yml 2022-05-02 11:38:39 -04:00
jvhagey
24dc2d2113 added tests 2022-05-02 11:30:19 -04:00