612 commits

Author	SHA1	Message	Date
Maxime Garcia	ea6fde0193	Merge pull request #252 from MaxUlysse/master_tiddit ... New module: tiddit	2021-02-25 09:34:33 +01:00
MaxUlysse	f62196a4a6	feat: add tiddit_sv module	2021-02-24 15:59:10 +01:00
JoseEspinosa	e9fc285967	Fix conda version declaration	2021-02-24 15:52:25 +01:00
Harshil Patel	50b98d56a1	Merge pull request #246 from drpatelh/master ... Update iVar modules	2021-02-24 13:00:05 +00:00
drpatelh	1094af2206	Add missing docs	2021-02-24 12:54:45 +00:00
Harshil Patel	ca4b4eb78e	Merge pull request #248 from JoseEspinosa/fix_bcftools ... Add missing requirements to bcftools modules	2021-02-24 12:51:39 +00:00
FriederikeHanssen	4673c119c7	resolve merge conflicts	2021-02-24 10:03:16 +01:00
JoseEspinosa	ec674bb127	Add label to bcftools processes	2021-02-24 09:47:54 +01:00
JoseEspinosa	823a631afc	Fix tools entry on yml	2021-02-24 09:47:36 +01:00
Jose Espinosa-Carrasco	8f4363ccb5	Merge pull request #247 from JoseEspinosa/bcftools-mpileup ... Add bcftools mpileup module	2021-02-24 09:24:43 +01:00
JoseEspinosa	af7bc743bf	Correct yml file, add fasta to input and correct vcf on output	2021-02-24 09:15:18 +01:00
Harshil Patel	5287fe5f95	Merge pull request #245 from phue/bismark_deduplicate ... add bismark/deduplicate + tests	2021-02-23 21:08:24 +00:00
Harshil Patel	4703a60443	Merge pull request #220 from phue/bwameth ... add bwameth modules	2021-02-23 21:01:54 +00:00
JoseEspinosa	138be9f918	Adding label to the bcftools-mpileup process	2021-02-23 21:52:15 +01:00
drpatelh	89cd71309c	Output log file for MultiQC	2021-02-23 20:36:23 +00:00
drpatelh	9098ba41c8	Update ivar consensus	2021-02-23 20:36:03 +00:00
JoseEspinosa	035443b6e0	Add bcftools-mpileup module	2021-02-23 19:05:26 +01:00
phue	e73bda26f5	add bismark/deduplicate + tests	2021-02-23 18:02:16 +01:00
FriederikeHanssen	bf58948dad	remove todos, describe in/output	2021-02-23 15:41:11 +01:00
FriederikeHanssen	4e9d728108	allow fq.gz or gastq.gz as in/output	2021-02-23 15:40:22 +01:00
FriederikeHanssen	12137d6f3e	Remove trialing whitespace	2021-02-23 15:00:21 +01:00
FriederikeHanssen	e251a3bed5	Remove todos	2021-02-23 14:58:09 +01:00
FriederikeHanssen	13733b2581	Add beautiful md5sums	2021-02-23 14:57:07 +01:00
FriederikeHanssen	5e365d5eff	Make all these tests pass	2021-02-23 14:09:46 +01:00
FriederikeHanssen	25a2a16f2d	Try to make a single test pass	2021-02-23 13:34:50 +01:00
kevinmenden	3fee38ee2d	added gatk4 revertsam	2021-02-22 15:21:39 +01:00
kevinmenden	efd60d94ee	adding revertsam/ fix typo in mergevcfs	2021-02-22 15:10:20 +01:00
kevinmenden	69d7bb4fca	reformatted input to tuple	2021-02-22 13:31:54 +01:00
phue	bf0e0d857d	bwameth/align: fix fasta name retrieval ... apparently bwameth doesn't like './' in front of the filepath? I have no idea. This works however	2021-02-20 13:12:43 +01:00
phue	c67e591caf	apply suggestions from review ... thanks @drpatelh	2021-02-20 12:51:01 +01:00
kevinmenden	bb5c0ceca5	adding SplitNCigarReads	2021-02-19 14:59:29 +01:00
Kevin Menden	0202162b17	Merge branch 'master' into gatk4-mergevcfs	2021-02-19 14:11:30 +01:00
kevinmenden	02abe106ec	added optional reference dictionary as input	2021-02-19 14:09:32 +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
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
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	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
phue	b5b259a2d9	add qualimap/bamqc + test	2021-02-17 17:34:51 +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	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
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
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
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	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	d6d34a4b5b	Merge pull request #177 from MaxUlysse/master_gatk_createsequencedictionary ... Add gatk/createsequencedictionary	2021-02-16 22:21:38 +00:00
Harshil Patel	a6d6c0b973	Update software/gatk/createsequencedictionary/main.nf	2021-02-16 22:08:11 +00:00
Harshil Patel	7c64e70c9e	Update software/gatk/createsequencedictionary/meta.yml	2021-02-16 22:07:51 +00:00
Harshil Patel	e558d5fb57	Merge pull request #174 from andersgs/ivar_consensus_fix ... ivar consensus: Add save mpileup as optional in output directive	2021-02-16 22:04:38 +00:00
MaxUlysse	6a147b8aaa	chores: replace bcftools/bgzip by tabix/bgzip cf #179	2021-02-16 19:11:36 +01:00
MaxUlysse	edf5fa3cf6	fix: merge bcftools/tabix and htslib/tabix into tabix/tabix	2021-02-16 18:27:13 +01:00
MaxUlysse	f660324508	chores: move file	2021-02-16 18:20:43 +01:00
MaxUlysse	274897f1fd	fix: ECLint: Wrong line endings or new final newline	2021-02-16 17:11:50 +01:00
MaxUlysse	5e71dc94d6	fix: make HTSLIB_TABIX more modular	2021-02-16 17:06:55 +01:00
MaxUlysse	10524e3515	chores: add modules for htslib/tabix	2021-02-16 14:47:53 +01:00
MaxUlysse	28dc9227d7	fix: remove memory requirements and simplify URI	2021-02-16 13:54:40 +01:00
MaxUlysse	30e3f2c5f5	fix: ECLint check: trailing whitespace	2021-02-16 13:42:34 +01:00
MaxUlysse	7f35a1742d	chores: add gatk/createsequencedictionary module	2021-02-16 13:40:06 +01:00
Maxime Garcia	d8706c12b3	Update meta.yml ... typo	2021-02-16 11:22:15 +01:00
Anders Goncalves da Silva	fd854c333e	Add save mpileup as optional in output directive	2021-02-15 21:07:31 -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	7cae9b1842	Add gff to meta yaml	2021-02-15 20:49:37 -08:00
Anders Goncalves da Silva	26189f4132	Change ternary expressions back to traditional format ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:56:22 -08:00
Anders Goncalves da Silva	4f8ab8bd69	Rename gff to features ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:53:30 -08:00
Anders Goncalves da Silva	8c483d4c6a	Add gff as input for proper staging ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:53:13 -08:00
Anders Goncalves da Silva	6259b72081	Fix output format ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:52:30 -08:00
Anders Goncalves da Silva	ef1e1b2539	Fix indentation ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-15 19:51:45 -08:00
Harshil Patel	8eb3acc43f	Merge pull request #171 from JoseEspinosa/mosdepth ... Add mosdepth module	2021-02-15 23:13:01 +00:00
Harshil Patel	f97c78b3fb	Update software/mosdepth/main.nf	2021-02-15 22:49:53 +00:00
Anders Goncalves da Silva	f841483a70	Fix URL for containers	2021-02-15 13:23:35 -08:00
Anders Goncalves da Silva	e8d1171b5d	Make gff a param and not an optional input	2021-02-15 11:50:52 -08:00
Anders Goncalves da Silva	9e3c4e598c	Add meta to ivar variants	2021-02-15 09:29:10 -08:00
Anders Goncalves da Silva	2fe3210f88	Add ivar variants	2021-02-15 09:27:59 -08:00
JoseEspinosa	6e92a6a080	Adding mosdepth module	2021-02-15 14:33:44 +01:00
Maxime Garcia	ec0bf0145e	Merge branch 'master' into master_bwa-mem2	2021-02-15 13:08:52 +01:00
Harshil Patel	4af9417b6d	Update software/ivar/trim/main.nf	2021-02-13 08:20:06 +00:00
Harshil Patel	a5686ed14e	Update software/ivar/trim/main.nf	2021-02-13 08:19:55 +00:00
Harshil Patel	25f3d46f68	Update software/ivar/trim/meta.yml	2021-02-13 08:17:03 +00:00
Anders Goncalves da Silva	bbdca4fa76	Fix output files	2021-02-12 16:14:46 -08:00
Anders Goncalves da Silva	7c9766962d	Add ivar trim meta.yml	2021-02-12 16:02:48 -08:00
Anders Goncalves da Silva	6dca7799e6	Add ivar trim	2021-02-12 16:02:10 -08:00
Harshil Patel	63a20e7b5c	Merge pull request #168 from JoseEspinosa/bcftools_merge ... Add bcftools merge module	2021-02-12 23:20:30 +00:00
Harshil Patel	c0d128fd39	Update software/bcftools/merge/main.nf	2021-02-12 23:16:52 +00:00
Anders Goncalves da Silva	9268851cde	Remove samtools option ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 15:09:50 -08:00
Anders Goncalves da Silva	1f66954180	Relabel input parameter ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 15:09:35 -08:00
JoseEspinosa	5313698705	Add bcftools merge module	2021-02-13 00:08:57 +01:00
Harshil Patel	0580fd8ded	Update software/ivar/consensus/main.nf	2021-02-12 23:02:04 +00:00
Harshil Patel	9e4539473e	Update software/ivar/consensus/main.nf	2021-02-12 23:01:53 +00:00
Harshil Patel	bc5e073cdb	Update software/ivar/consensus/main.nf	2021-02-12 22:57:06 +00:00
Anders Goncalves da Silva	cb19c7b056	Fix trailing whitespace	2021-02-12 14:46:13 -08:00
Anders Goncalves da Silva	b08bf1ea5c	Remove ref to conda build and additional params	2021-02-12 14:43:50 -08:00
Anders Goncalves da Silva	24b212318b	Merge branch 'master' into ivar-consensus	2021-02-12 11:51:24 -08:00
Anders Goncalves da Silva	bfc13d3379	Add options to make samtools more flexible	2021-02-12 11:50:33 -08:00
Anders Goncalves da Silva	a4bba006bd	Add reference fasta as input	2021-02-12 11:26:55 -08:00
Anders Goncalves da Silva	6b22bb9782	Add meta.yml	2021-02-12 11:25:40 -08:00
JoseEspinosa	0688230863	Revert since fixes to test were not working ... This reverts commit d7a219e88d.	2021-02-12 18:02:32 +01:00
JoseEspinosa	8e23e1839d	Trying to fix tests	2021-02-12 17:56:51 +01:00
JoseEspinosa	6e8b63fc26	Add cat fastq module	2021-02-12 17:22:07 +01:00
MaxUlysse	9c98194d3c	chores: remove fasta file from bwamem2 mem process	2021-02-12 16:00:59 +01:00
MaxUlysse	0afddf6ca4	fix: CI is working	2021-02-12 15:24:09 +01:00
Maxime Garcia	c1ff201518	Apply suggestions from code review ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-12 13:24:10 +01:00
MaxUlysse	6b34ddf239	chores: bwa-mem2 -> bwamem2	2021-02-12 13:08:44 +01:00
MaxUlysse	a910d1a608	chores: add bwa-mem2 index + mem	2021-02-12 13:00:02 +01:00
Maxime Garcia	27be87ac72	Merge pull request #135 from drpatelh/bwa ... Update indices syntax for BWA index and mem modules	2021-02-12 12:45:38 +01:00
Anders Goncalves da Silva	e9aa037e7b	Add function to enable output of mpileup ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:02:06 -08:00
Anders Goncalves da Silva	06770d5f02	Specify the exact bioconda recipe build ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:01:25 -08:00
Anders Goncalves da Silva	362a630f8b	Change suffix of mpileup ouput file ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:00:54 -08:00
Anders Goncalves da Silva	884c4658b8	Make mpileup saving optional ... Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>	2021-02-10 10:00:22 -08:00
Jose Espinosa-Carrasco	1e771ac8a0	Merge pull request #164 from drpatelh/fixes ... Add missing build ids and rename *.txt channels	2021-02-10 14:19:00 +01:00
drpatelh	b9afca2b05	Underscore not .	2021-02-10 12:53:17 +00:00
drpatelh	d2508e3c03	Amend prefix for bcftools stats	2021-02-10 12:51:47 +00:00
drpatelh	e63279e6a2	Pin pangoLearn version	2021-02-10 10:28:27 +00:00
drpatelh	b03846600d	Tidy up	2021-02-09 23:26:45 +00:00
drpatelh	6795fe04b8	Rename output channel	2021-02-09 23:26:18 +00:00
drpatelh	2b9129b3f9	Change txt channel output	2021-02-09 23:09:22 +00:00
drpatelh	d50d070c06	Change txt channel output	2021-02-09 23:09:18 +00:00
drpatelh	0b33b6d081	Add missing build ids	2021-02-09 23:03:13 +00:00
JoseEspinosa	e8dc199dc8	Adding conda build to blast modules	2021-02-09 23:04:12 +01:00
JoseEspinosa	2fa14f2ec8	Adding conda build to bcftools modules	2021-02-09 23:00:19 +01:00
Harshil Patel	3f431014a4	Update software/bedtools/getfasta/main.nf	2021-02-09 21:34:40 +00:00
Anders Goncalves da Silva	8f546a1f95	Add ivar consensus	2021-02-09 10:26:35 -08:00
JoseEspinosa	68b85d9191	Merge remote-tracking branch 'upstream/master' into bedtools_getfasta	2021-02-09 18:23:24 +01:00
JoseEspinosa	e118bc049a	Add bedtools getfasta module	2021-02-09 17:56:51 +01:00
JoseEspinosa	12ae7b0bff	Adding blast blastn module	2021-02-09 16:58:36 +01:00
JoseEspinosa	c23b355b35	Add blast makeblastdb module	2021-02-09 15:44:34 +01:00
JoseEspinosa	c93e96101a	Add untar module	2021-02-09 11:50:32 +01:00
JoseEspinosa	20771ae1bc	Remove meta from input/output meta.yml	2021-02-09 11:02:31 +01:00
JoseEspinosa	b09416a0d0	Correcting meta.yml	2021-02-09 10:51:57 +01:00
JoseEspinosa	f7f06dd6e8	Add gunzip module	2021-02-09 10:05:55 +01:00
Harshil Patel	46e5df2cf7	Merge pull request #151 from drpatelh/bedtools ... Follow up fixes for bedtools modules added in #79	2021-02-09 01:54:31 +00:00
Harshil Patel	84cf5ea2ef	Merge pull request #153 from JoseEspinosa/bedtools_maskfasta ... Add bedtools maskfasta module	2021-02-08 23:11:00 +00:00
JoseEspinosa	02d10c25a3	Add bedtools maskfasta module	2021-02-08 23:41:10 +01:00
JoseEspinosa	f4e322f88d	Merging upstream changes ... # Conflicts: # .github/filters.yml	2021-02-08 18:09:41 +01:00
JoseEspinosa	fe412797dd	Adressing general comments on PR #134	2021-02-08 15:11:36 +01:00
JoseEspinosa	5071bf5914	Merge remote-tracking branch 'upstream/master' into bcftools_viralrecon	2021-02-08 10:45:57 +01:00
drpatelh	c9cfdd31f3	Fix barfing linters	2021-02-08 00:57:06 +00:00