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2648 commits 30 branches 0 tags 142 MiB
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1356 commits

Author SHA1 Message Date
Thomas A. Christensen II
4eca77d63b Add CAT_FASTQ tests for a single pair of files 
The test is written to expect that the input files will be renamed, but the
contents will remain the same, i.e. the test uses the md5 hash of the input
files.
 2022-05-16 18:03:23 -05:00
Thomas A. Christensen II
0df133f04e Add CAT_FASTQ tests for a single non-paired file 
The test is written to expect that the input file will be renamed, but the
contents will remain the same, i.e. the test uses the md5 hash of the input
file.
 2022-05-16 18:03:23 -05:00
Veit Schwämmle
74a1c1400e
Merge branch 'master' into maxquant 2022-05-16 13:26:35 +02:00
Jasmin F
982c9183fa
Merge branch 'master' into antismashlite 2022-05-16 11:42:44 +02:00
Jasmin F
adcfae6cd4
Merge branch 'master' into antismashlite 2022-05-16 10:38:01 +02:00
Rike
eb841d4ea0 revert markduplciatespark changes 2022-05-16 10:33:01 +02:00
FriederikeHanssen
8b4d021189
Merge branch 'master' into gatk_426 2022-05-16 09:50:13 +02:00
Matthias De Smet
5a2e303522 add PE sorted test 2022-05-13 19:16:50 +02:00
Matthias De Smet
04f82d4d34 fix test name 2022-05-13 15:32:14 +02:00
Matthias De Smet
cbc47767f7 add sort option to bowtie2 2022-05-13 15:26:41 +02:00
Nicolas Vannieuwkerke
a72f06dfe8 removed versions checksum 2022-05-13 14:27:59 +02:00
nvnieuwk
1d4862ba60
Merge branch 'master' into new-module-gatk4/splitintervals 2022-05-13 13:47:20 +02:00
Nicolas Vannieuwkerke
8a17b6dd0e added gatk4/splitintervals 2022-05-13 13:46:34 +02:00
Chris Cheshire
ea55129ba3 Removed version file checksums 2022-05-13 12:20:41 +01:00
Chris Cheshire
9f6a1ae4a4
Merge branch 'master' into bowtie2-test-fix 2022-05-13 12:05:48 +01:00
Chris Cheshire
d816f2bc5d Reactivated all tests 2022-05-13 12:01:16 +01:00
Mahesh Binzer-Panchal
00826dc2e9
Merge branch 'master' into genomescope2 2022-05-13 11:28:47 +02:00
Mahesh Binzer-Panchal
5df0bcf1be
Update tests/modules/genomescope2/test.yml 
Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
 2022-05-13 11:27:42 +02:00
FriederikeHanssen
868150e1af
Merge branch 'master' into gatk_426 2022-05-12 19:33:07 +02:00
Rike
99880654bf add output default bam 2022-05-12 18:06:15 +02:00
Rike
8792d102ee fix test input 2022-05-12 17:37:06 +02:00
Rike
a694267b4b fix empty index input 2022-05-12 17:01:03 +02:00
Rike
b3bd55da76 getpileupsummaries requires intervals files 2022-05-12 16:51:17 +02:00
Rike
15fbf21b28 double tmpdir args removed, porb leftover after massive refactor where we decided to make it mandatory everywhere 2022-05-12 16:16:53 +02:00
Rike
fef5434c4c Update md5sums 2022-05-12 16:07:12 +02:00
Jasmin F
85b3c2bcf2
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-12 15:28:19 +02:00
James A. Fellows Yates
3c02e6056c
Merge branch 'master' into antismashlite 2022-05-12 14:53:52 +02:00
jasmezz
d2ef476321 Fix Prettier linting error 2022-05-12 12:19:50 +02:00
jasmezz
37cc6f250b Fixed test.yml 2022-05-12 12:14:19 +02:00
Chris Cheshire
90c67794bf Added extra tests but error with collection 2022-05-12 10:01:33 +01:00
jasmezz
bd4b70439b Streamlined some output channels, formatted tests main.nf 2022-05-12 10:56:48 +02:00
Moritz E. Beber
74b11ccc44 refactor: rename and update subworkflow 2022-05-11 19:24:16 +02:00
Matthias De Smet
dcf9c07fc9
Merge branch 'master' into update/bowtie2-align 2022-05-11 19:08:23 +02:00
Moritz E. Beber
98d8a741ec tests: add missing paths to config 2022-05-11 18:17:27 +02:00
Moritz E. Beber
888620063b tests: delete settings for conda 2022-05-11 17:44:49 +02:00
Moritz E. Beber
b2dbaa9930 refactor: rename module 2022-05-11 17:33:45 +02:00
Moritz E. Beber
23091aabda refactor: move files to custom section 2022-05-11 17:33:45 +02:00
Moritz E. Beber
a83dd33a7e tests: use remove settings file 2022-05-11 17:33:45 +02:00
Moritz E. Beber
e4551a9ab3 refactor: always output settings 2022-05-11 17:33:45 +02:00
Moritz E. Beber
64ff23f3c1 feat: add module that verifies NCBI settings 2022-05-11 17:33:45 +02:00
Harshil Patel
4e603393c3
Merge branch 'master' into update/bowtie2-align 2022-05-11 15:47:37 +01:00
Jasmin F
853e3ec087
Remove commented code 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-05-11 15:56:10 +02:00
Mahesh Binzer-Panchal
fbe2f85e7b Fix path 2022-05-11 13:53:38 +00:00
Matthias De Smet
94e8c3a882
Update tests/modules/bowtie2/align/test.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:56:03 +02:00
Matthias De Smet
0d00452eca
Update tests/modules/bowtie2/align/test.yml 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:55:45 +02:00
Matthias De Smet
dcffd93875
Merge branch 'master' into update/bowtie2-align 2022-05-11 13:34:24 +02:00
CMGG ICT Team
3ae8cbfad7 bowtie2: remove code duplication 2022-05-11 13:32:56 +02:00
Moritz E. Beber
0cdf7767a7 refactor: require NCBI user settings always 2022-05-11 13:02:52 +02:00
Moritz E. Beber
eae7161a32 tests: add settings input or not and test all branches 2022-05-11 12:47:54 +02:00
Mahesh Binzer-Panchal
00fcdd0cba
Merge branch 'master' into genomescope2 2022-05-11 12:42:39 +02:00