323 commits

Author	SHA1	Message	Date
kevinmenden	bd8ba42a8d	added gatk4 SamToFastq	2021-02-19 12:41:29 +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
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
Michael L Heuer	206b605666	Add module for seqwish/induce	2021-02-17 11:19:47 -06:00
phue	b5b259a2d9	add qualimap/bamqc + test	2021-02-17 17:34:51 +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
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	412172cda6	Merge pull request #180 from MaxUlysse/master_tabix_bgzip ... Replace bcftools/bgzip by tabix/bgzip	2021-02-16 23:32:23 +00:00
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
Harshil Patel	b07ad23efa	Merge pull request #179 from MaxUlysse/master_htslib_tabix ... Replace bcftools/tabix by tabix/tabix	2021-02-16 22:30:45 +00:00
Harshil Patel	4f11064ae2	Update tests/software/tabix/bgzip/main.nf	2021-02-16 22:30:06 +00:00
Harshil Patel	8dd6d1d38a	Update tests/software/tabix/bgzip/main.nf	2021-02-16 22:29:13 +00:00
Harshil Patel	d6d34a4b5b	Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary ... Add gatk/createsequencedictionary	2021-02-16 22:21:38 +00:00
MaxUlysse	6a147b8aaa	chores: replace bcftools/bgzip by tabix/bgzip cf #179	2021-02-16 19:11:36 +01:00
MaxUlysse	5a144d6213	fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix	2021-02-16 18:35:32 +01:00
MaxUlysse	f660324508	chores: move file	2021-02-16 18:20:43 +01:00
MaxUlysse	5e71dc94d6	fix: make HTSLIB_TABIX more modular	2021-02-16 17:06:55 +01:00
MaxUlysse	fa34f806d2	chores: add bgzip files for tests	2021-02-16 17:06:09 +01:00
MaxUlysse	10524e3515	chores: add modules for htslib/tabix	2021-02-16 14:47:53 +01:00
MaxUlysse	4968458b6c	chores: add cpus, memory and time requirements to limit resource consumption	2021-02-16 14:18:29 +01:00
MaxUlysse	763800a0e2	fix: correct md5sum	2021-02-16 13:54:54 +01:00
MaxUlysse	28dc9227d7	fix: remove memory requirements and simplify URI	2021-02-16 13:54:40 +01:00
MaxUlysse	053dd6ee1b	add minimal cpu,memory and time requirements	2021-02-16 13:40:22 +01:00
MaxUlysse	7f35a1742d	chores: add gatk/createsequencedictionary module	2021-02-16 13:40:06 +01:00
Anders Goncalves da Silva	eeedb959c9	Clean out comments	2021-02-15 21:04:17 -08:00
Anders Goncalves da Silva	b99972f3a0	Move params to nextflow invocation	2021-02-15 20:59:45 -08:00
Anders Goncalves da Silva	89f65e0875	Merge branch 'master' into ivar-variant	2021-02-15 20:50:35 -08:00
Anders Goncalves da Silva	c12a558f15	Add tests without mpileup	2021-02-15 20:49:27 -08:00
Anders Goncalves da Silva	3188b8e30e	Add explicit gff is false param ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:55:34 -08:00
Anders Goncalves da Silva	ee4c2828a0	Update gff assignment to string ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:55:12 -08:00
Anders Goncalves da Silva	39401ccd07	Add gff as input ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:54:36 -08:00
Anders Goncalves da Silva	8b6989f2d7	Add gff as input ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:54:19 -08:00
Harshil Patel	8eb3acc43f	Merge pull request #171 from JoseEspinosa/mosdepth ... Add mosdepth module	2021-02-15 23:13:01 +00:00
Anders Goncalves da Silva	9a5aa0f145	Fix tests to work with gff param	2021-02-15 11:51:04 -08:00
Anders Goncalves da Silva	4af7414419	Add tests for ivar variants	2021-02-15 09:29:40 -08:00
JoseEspinosa	6e92a6a080	Adding mosdepth module	2021-02-15 14:33:44 +01:00