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Author	SHA1	Message	Date
kevinmenden	c0693fa3db	remove whitespace	2021-02-19 13:30:40 +01:00
kevinmenden	c288e081b4	initial commit adding mergevcfs	2021-02-19 13:29:08 +01:00
Kevin Menden	5c325f2942	Merge branch 'master' into master	2021-02-19 13:08:43 +01:00
Kevin Menden	134f0ac78c	Merge pull request #236 from KevinMenden/gatk4-bamtofastq ... added gatk4 SamToFastq	2021-02-19 13:07:10 +01:00
kevinmenden	908e55ee5c	fixed tag	2021-02-19 12:46:59 +01:00
kevinmenden	bd8ba42a8d	added gatk4 SamToFastq	2021-02-19 12:41:29 +01:00
kevinmenden	6dcaf5ffc8	add gatk4 bedtointervallist	2021-02-19 11:26:31 +01:00
MaxUlysse	eaff4eb0ff	fix: order alphabetically	2021-02-19 10:56:04 +01:00
Harshil Patel	01c0d335ca	Merge pull request #223 from phue/bismark_genome_preparation ... add bismark/genome_preparation + test	2021-02-18 19:08:00 +00:00
phue	a963c67481	bwameth: pass genome index as directory ... instead of single files	2021-02-18 11:51:36 +01:00
phue	0d8f5f0572	add bismark/genome_preparation + tests	2021-02-18 10:56:36 +01:00
Patrick Hüther	dba295155e	Merge pull request #219 from phue/qualimap_bamqc ... add qualimap/bamqc + test	2021-02-18 10:09:03 +01:00
phue	0606c06a25	qualimap/bamqc: remove unneeded variable definition ... can just use task.cpus directly	2021-02-18 10:00:49 +01:00
Harshil Patel	5695e4ccce	Merge pull request #222 from phue/methyldackel ... add methyldackel modules	2021-02-17 22:17:26 +00:00
Harshil Patel	ecd26b388d	Merge pull request #221 from heuermh/seqwish ... Add module for seqwish/induce	2021-02-17 22:14:49 +00:00
phue	52b00d4286	add methyldackel/mbias + tests	2021-02-17 19:27:57 +01:00
phue	5ad7c6bc51	add methyldackel/extract + tests + testdata	2021-02-17 19:18:55 +01:00
phue	1a414261c4	bwameth/align: update checksums	2021-02-17 18:35:39 +01:00
phue	84a5da0d91	add bwameth/align module + tests	2021-02-17 18:23:11 +01:00
Michael L Heuer	206b605666	Add module for seqwish/induce	2021-02-17 11:19:47 -06:00
phue	180b1cf36b	add bwameth/index module + test	2021-02-17 18:03:48 +01:00
Patrick Hüther	78cf182ed4	Merge pull request #218 from phue/samtools_faidx ... add samtools/faidx + tests	2021-02-17 17:37:16 +01:00
phue	b5b259a2d9	add qualimap/bamqc + test	2021-02-17 17:34:51 +01:00
FriederikeHanssen	5f9aa7264e	Add tests	2021-02-17 17:25:41 +01:00
Patrick Hüther	0cbe0a4173	Update tests/software/samtools/faidx/main.nf ... Co-authored-by: Maxime Garcia <maxime.garcia@scilifelab.se>	2021-02-17 17:24:50 +01:00
FriederikeHanssen	2654c52ed1	Use list of reads as input, similar to dedup/extract	2021-02-17 17:15:02 +01:00
FriederikeHanssen	bedc2972eb	Add seqkit split2	2021-02-17 17:09:24 +01:00
phue	a156bdfc03	faidx: add filter	2021-02-17 17:01:22 +01:00
phue	aafc6949d3	faidx: add process label	2021-02-17 16:56:45 +01:00
phue	3b1d126a0e	add samtools/faidx + tests	2021-02-17 16:46:34 +01:00
Harshil Patel	ed573db194	Merge pull request #184 from MaxUlysse/master_fix_ci ... fix: update checksum or filename	2021-02-17 10:54:38 +00:00
Harshil Patel	4d656c8f5f	Merge pull request #181 from drpatelh/fixes ... Fix tests for iVar variants	2021-02-17 10:08:57 +00:00
MaxUlysse	28fb5e8cbd	fix: update checksum or filename	2021-02-17 01:34:50 +01:00
Harshil Patel	f677a6a05e	Merge pull request #183 from nf-core/MaxUlysse-patch-1 ... Update .markdownlint.yml	2021-02-17 00:20:51 +00:00
Harshil Patel	67d4dab632	Merge pull request #182 from drpatelh/rm_build ... Remove Conda build ids for all modules	2021-02-17 00:20:00 +00:00
Maxime Garcia	4c511757f3	Update .markdownlint.yml ... fix typo	2021-02-17 01:15:21 +01:00
drpatelh	d47f9bb909	@kevinmenden sanity fix	2021-02-16 23:58:52 +00:00
drpatelh	dcc580e4fb	Remove Conda build ids for all modules	2021-02-16 23:58:23 +00:00
Maxime Garcia	842173be9f	Merge pull request #175 from MaxUlysse/master_ISSUE_TEMPLATE ... fix: add guidelines to PRs and issues	2021-02-17 00:36:35 +01:00
MaxUlysse	ebb6d5de1f	fix: Apply suggestions from code review	2021-02-17 00:34:55 +01:00
Harshil Patel	412172cda6	Merge pull request #180 from MaxUlysse/master_tabix_bgzip ... Replace bcftools/bgzip by tabix/bgzip	2021-02-16 23:32:23 +00:00
Maxime Garcia	75d1483417	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-17 00:32:06 +01:00
drpatelh	c6a0976f52	Fix tests for iVar variants	2021-02-16 23:29:15 +00:00
MaxUlysse	596bb18394	fix: rename file to input and gz, plus fix tests	2021-02-17 00:28:32 +01:00
Harshil Patel	a282ecd8c7	Merge pull request #172 from andersgs/ivar-variant ... Add ivar variants	2021-02-16 23:20:30 +00:00
Harshil Patel	cf2f0762aa	Update main.nf	2021-02-16 23:06:26 +00:00
Harshil Patel	7c276d2974	Update tests/software/ivar/variants/main.nf	2021-02-16 23:01:27 +00:00
Harshil Patel	27020105aa	Update tests/software/ivar/variants/main.nf	2021-02-16 23:00:30 +00:00
Harshil Patel	de90d371dc	Update tests/software/ivar/variants/main.nf	2021-02-16 22:58:38 +00:00
Harshil Patel	23987bdad0	Update tests/software/ivar/variants/main.nf	2021-02-16 22:57:47 +00:00