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Author	SHA1	Message	Date
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	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
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
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
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
Mahesh Binzer-Panchal	00fcdd0cba	Merge branch 'master' into genomescope2	2022-05-11 12:42:39 +02:00
Mahesh Binzer-Panchal	d54cf467f4	Update outputs and test data set	2022-05-11 10:42:17 +00:00
Harshil Patel	79bf60fa11	Merge pull request #1631 from nf-core/refactor-prefetch ... Refactor prefetch	2022-05-11 11:29:02 +01:00
Harshil Patel	7be7f404d5	Merge branch 'master' into refactor-prefetch	2022-05-11 11:28:02 +01:00