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Author SHA1 Message Date
Rike
b3bd55da76 getpileupsummaries requires intervals files 2022-05-12 16:51:17 +02:00
Rike
f40cfefc08 leftover fixes from refactoring 2022-05-12 16:47:17 +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
Rike
fd7ee6799a update version also for spark containers 2022-05-12 15:55:11 +02:00
Rike
169b2b96c1 update gatk version 2022-05-12 15:45:21 +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
JIANHONG OU
6b960f0e75 fix the typo in motus_profile. 2022-05-12 09:20:32 -04:00
James A. Fellows Yates
3c02e6056c
Merge branch 'master' into antismashlite 2022-05-12 14:53:52 +02:00
Harshil Patel
be0f022053
Merge pull request #1648 from nf-core/refactor-sra-fastq 
refactor: rename and update subworkflow
 2022-05-12 11:26:15 +01:00
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
Chris Cheshire
4bb0423a1d Merge remote-tracking branch 'nf-core/master' 2022-05-12 08:57:56 +01:00
JIANHONG OU
a2dbef3de3 remove the wrong quotes for motus_profile. 2022-05-11 17:49:12 -04:00
JIANHONG OU
aca4b48842 Merge branch 'motus_profile' of github.com:jianhong/modules into motus_profile 2022-05-11 14:23:25 -04:00
JIANHONG OU
ae81311a78 fix the typo when using getExtension for motus_profile. 2022-05-11 14:23:09 -04:00
Moritz E. Beber
74b11ccc44 refactor: rename and update subworkflow 2022-05-11 19:24:16 +02:00
Matthias De Smet
1dccf12077
Merge pull request #1645 from matthdsm/update/bowtie2-align 
bowtie2: remove code duplication
 2022-05-11 19:12:23 +02:00
Matthias De Smet
dcf9c07fc9
Merge branch 'master' into update/bowtie2-align 2022-05-11 19:08:23 +02:00
Harshil Patel
4aaff98c49
Merge pull request #1630 from nf-core/add-ncbi-settings 
feat: add module that verifies NCBI settings
 2022-05-11 17:51:24 +01:00
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
Mahesh Binzer-Panchal
0199d0efd2
Merge branch 'master' into kat_hist 2022-05-11 16:56:29 +02:00
Harshil Patel
4e603393c3
Merge branch 'master' into update/bowtie2-align 2022-05-11 15:47:37 +01:00
Matthias De Smet
c8d3de2ad9
restore samtools cmd to defaults 2022-05-11 16:17:30 +02:00
Mahesh Binzer-Panchal
64dad04b9b
Merge pull request #1646 from mahesh-panchal/fix_test_config 
Fix path
 2022-05-11 15:58:55 +02:00
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
bcd7fe55b1
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:59:03 +02:00
Matthias De Smet
9097abf277
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:58:58 +02:00
Matthias De Smet
971a889e2a
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:57:27 +02:00
Matthias De Smet
b456d8fa0a
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:57:19 +02:00
Matthias De Smet
ff4b297827
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:57:11 +02:00
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
9dd083fa94
Update modules/bowtie2/align/main.nf 
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
 2022-05-11 13:55:55 +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
Harshil Patel
9602b989eb
Merge pull request #1632 from nf-core/refactor-fasterq-dump 
Refactor fasterq dump
 2022-05-11 12:14:22 +01:00
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
Moritz E. Beber
d4f13ebfff refactor: create new settings input 2022-05-11 12:47:54 +02:00
Moritz E. Beber
5d593bdb45 docs: correct license and input description 2022-05-11 12:47:54 +02:00