124 commits

Author	SHA1	Message	Date
James Fellows Yates	e5c6db96c8	update all modules to make templaite compatible	2022-12-23 17:23:05 +01:00
Sofia Stamouli	35b296e5fd	Merge pull request #202 from nf-core/nf-core-template-merge-2.7.2 ... Important! Template update for nf-core/tools v2.7.2	2022-12-21 09:18:40 +01:00
James Fellows Yates	612f532fb2	Bump KrakenUniq version	2022-12-20 20:08:12 +01:00
Sofia Stamouli	d691b89727	Merge branch 'dev' into nf-core-template-merge-2.7.2	2022-12-20 15:14:41 +01:00
James A. Fellows Yates	25bb4304e8	Merge pull request #187 from nf-core/revert-pep ... Revert PEP validation back to python samplesheet check	2022-12-20 15:03:18 +01:00
nf-core-bot	ab591e01ff	Template update for nf-core/tools version 2.7.2	2022-12-19 12:10:58 +00:00
James Fellows Yates	0bdc119f9c	Include falco patch	2022-12-15 13:27:41 +01:00
James Fellows Yates	3b86a22556	Fix falco publication names	2022-12-15 12:57:49 +01:00
James Fellows Yates	e31e7d3172	Update mOTUs to 3.0.3	2022-12-12 15:42:01 +01:00
James Fellows Yates	3df0a383da	Update combine bracken outputs to include meta for publishing purposes	2022-12-12 10:10:24 +01:00
James Fellows Yates	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +01:00
James Fellows Yates	8939ce3e20	Start adding bracken/combinebrackenreports (need smodule update)	2022-12-11 16:52:34 +01:00
James Fellows Yates	d8751787ac	Update bracken so parameters come directly from database args	2022-12-07 07:27:40 +01:00
James A. Fellows Yates	a34b240dfc	Merge pull request #174 from nf-core/malt-update ... Update MALT	2022-12-01 13:58:30 +01:00
James A. Fellows Yates	4f6eb6fd75	Merge pull request #153 from mjamy/add-krakenuniq-module ... Add krakenuniq module	2022-12-01 09:03:29 +01:00
Moritz E. Beber	af8ce2cbfd	chore: update krakenuniq	2022-11-29 10:27:35 +01:00
James Fellows Yates	131b39aa8b	Fix linting	2022-11-24 15:49:06 +01:00
James Fellows Yates	9feb6c2db6	Update MALT	2022-11-24 14:44:04 +01:00
James Fellows Yates	a383c9ae40	Remove the join	2022-11-22 13:39:21 +01:00
James Fellows Yates	cacd7d3128	Not just in stub	2022-11-22 13:33:13 +01:00
James Fellows Yates	e8de006ed6	With a join	2022-11-22 13:27:49 +01:00
James Fellows Yates	ebfc84e235	Does the grouping work if we have meta?	2022-11-22 13:26:54 +01:00
James A. Fellows Yates	bc671c547d	Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict ... Fix porechop conflict	2022-11-03 14:08:13 +01:00
James A. Fellows Yates	1f31f88635	Merge pull request #158 from nf-core/adapterremoval-fix ... Fix adapterremoval adapter conflict and add optional adapter list file	2022-11-03 11:36:14 +01:00
James Fellows Yates	d487a1ff2f	Addd FASTP adadapter list	2022-11-02 12:39:34 +01:00
Sofia Stamouli	3faea8aac5	Fix porechop conflict	2022-11-01 17:34:37 +01:00
Mahwash Jamy	3147a80a56	Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module	2022-10-31 15:36:57 +00:00
Sofia Stamouli	1bd6dbfe58	Add samtools stats for long-reads	2022-10-28 11:40:50 +02:00
Moritz E. Beber	bf89525bc2	Merge pull request #146 from nf-core/feat-bracken ... add Bracken to the profiling workflow	2022-10-27 17:35:06 +02:00
James A. Fellows Yates	76a662ecc5	Fix adapterremoval adapter conflict and add optional adapter list file	2022-10-27 12:17:19 +00:00
Mahwash Jamy	36e101a78b	Install krakenuniq module	2022-10-25 09:26:33 +00:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
Moritz E. Beber	4352d35937	chore: install Bracken module	2022-10-14 10:52:17 +02:00
James Fellows Yates	56bae85755	Remove necessity of patch	2022-10-11 12:38:18 +02:00
Moritz E. Beber	5f3dbd28de	fix: patch inputs to correspond to previous version	2022-10-05 13:51:15 +02:00
Moritz E. Beber	b407fbcdce	chore: force update all modules	2022-10-05 12:24:18 +02:00
Moritz E. Beber	fdb8a7f740	Merge branch 'devel' into nf-core-template-merge-2.6	2022-10-05 12:21:54 +02:00
nf-core-bot	51bacb00e6	Template update for nf-core/tools version 2.6	2022-10-05 03:30:53 +00:00
James A. Fellows Yates	3ca9058b9c	Merge pull request #133 from rafalstepien/add-pep-support ... Add working version of PEP-nf-core integration	2022-09-30 10:21:15 +02:00
Rafal Stepien	9349346864	Remove --pep parameter and leave just --input	2022-09-16 10:14:01 -04:00
James A. Fellows Yates	016efcb807	Merge branch 'dev' into metaphlan3/mergemetaphlantables	2022-09-16 16:02:38 +02:00
James Fellows Yates	c5cc21d29e	Update motus merge module to remove unused channel	2022-09-16 10:25:24 +02:00
James Fellows Yates	4e7857e2ed	Standardise mOTUs table merge	2022-09-16 08:36:34 +02:00
James A. Fellows Yates	cdb21d17b3	Merge branch 'dev' into metaphlan3/mergemetaphlantables	2022-09-15 13:08:57 +02:00
James Fellows Yates	21ae9d85c3	Ensure merge metaphlan3 tables happens on per database basis	2022-09-15 12:29:54 +02:00
Rafal Stepien	5f3eee9a4a	Add working version of PEP-nf-core integration	2022-09-14 14:28:48 -04:00
James Fellows Yates	abbbf9c7ab	Update to use tar module compatible for our test databases	2022-09-14 11:16:28 +02:00
James Fellows Yates	c8dbf5be47	Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU	2022-09-13 15:47:28 +02:00
James Fellows Yates	a764bc4807	Start works - need updated module though t have meta	2022-09-09 13:57:06 +02:00
James Fellows Yates	f087136ec9	use proper working FASTP module	2022-09-09 11:12:47 +02:00