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Author	SHA1	Message	Date
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
James Fellows Yates	d7fbe55849	Add KU to the test profiles and add id to KU processes	2022-11-29 14:19:01 +01:00
James A. Fellows Yates	3d949a803f	Merge pull request #175 from nf-core/schema-clean ... Fix schema location ofr fastqc/falco option	2022-11-29 11:49:27 +01:00
Moritz E. Beber	af8ce2cbfd	chore: update krakenuniq	2022-11-29 10:27:35 +01:00
James Fellows Yates	d6c0ebb4c6	Prettier	2022-11-29 10:14:33 +01:00
Moritz E. Beber	ddcf38de22	refactor: make mappings explicit	2022-11-29 10:14:20 +01:00
James Fellows Yates	f13185d98b	Fix schema location ofr fastqc/falco option	2022-11-29 10:13:46 +01:00
Sofia Stamouli	f8b769a8f0	Merge pull request #172 from genomic-medicine-sweden/update_samtools_stats ... Include the mapped reads in samtools stats	2022-11-23 10:21:47 +01:00
sofstam	481f90589c	Apply review suggestions	2022-11-23 09:08:22 +01:00
Moritz E. Beber	b6f5930b49	Merge pull request #171 from nf-core/chore-fail-slow ... chore: let all tests run to completion	2022-11-22 19:22:14 +01:00
sofstam	30af26a8b3	Include the mapped reads in samtools stats	2022-11-22 16:50:50 +01:00
James Fellows Yates	a383c9ae40	Remove the join	2022-11-22 13:39:21 +01:00
James Fellows Yates	06659af777	Remove flatten	2022-11-22 13:36:40 +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 Fellows Yates	21759807f7	Does flatten work?	2022-11-22 12:48:54 +01:00
James Fellows Yates	3102e40052	dump teh db	2022-11-22 12:46:26 +01:00
James Fellows Yates	557f2a4d96	Extra dump	2022-11-22 12:26:46 +01:00
James Fellows Yates	5caebcc6ab	Append to correct db	2022-11-22 12:21:59 +01:00
James Fellows Yates	52fc00802b	Correct meta name for db meta	2022-11-22 12:19:56 +01:00
James Fellows Yates	b8937748d3	Fix meta.id isssue	2022-11-22 12:18:52 +01:00
James Fellows Yates	db334c5185	Fix missing info	2022-11-22 12:17:08 +01:00
James Fellows Yates	0f298dca43	group krakenuniq reads by pairs or single end	2022-11-22 12:13:08 +01:00
Moritz E. Beber	6b538d658a	chore: let all tests run to completion	2022-11-22 10:13:10 +01:00
James A. Fellows Yates	10c72f1265	Merge pull request #169 from nf-core/diagram-update ... Update tubemap to include samtools stats	2022-11-06 10:15:56 +01:00
James Fellows Yates	f414f5dc9c	Add falco to tube map	2022-11-04 18:20:44 +01:00
James Fellows Yates	4275640d9b	update tubemap to include samtools stats	2022-11-04 15:24:15 +01:00
James A. Fellows Yates	67e264b7a9	Merge pull request #162 from genomic-medicine-sweden/short_reads_samtools ... Add samtools stats for short-reads	2022-11-04 14:39:29 +01:00
Sofia Stamouli	696edfb866	Apply prettier	2022-11-04 12:05:23 +01:00
Sofia Stamouli	d2195e9eda	Merge branch 'dev' into short_reads_samtools	2022-11-04 11:47:36 +01:00
Sofia Stamouli	79dd3930bb	Add samtools to README	2022-11-03 16:52:01 +01:00
James Fellows Yates	461482d22a	Try again wit hthe corret param	2022-11-03 15:02:22 +01:00
James Fellows Yates	93f38b14a8	Save report	2022-11-03 15:01:00 +01:00
James Fellows Yates	c5e5696f84	Fix parameter name	2022-11-03 14:58:03 +01:00
James Fellows Yates	c03a21c770	Merge branch 'add-krakenuniq-module' of github.com:mjamy/taxprofiler into add-krakenuniq-module	2022-11-03 14:56:43 +01:00
James Fellows Yates	21a76c2449	Fix cardinality issue	2022-11-03 14:56:26 +01:00
nf-core-bot	0c445759e4	[automated] Fix linting with Prettier	2022-11-03 13:42:39 +00:00
Sofia Stamouli	b5e6639f9d	Apply review suggestions	2022-11-03 14:12:05 +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 Fellows Yates	6459d8920f	Linting!	2022-11-03 14:05:43 +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 A. Fellows Yates	62f45c8be7	Update nextflow.config	2022-11-03 10:03:27 +01:00
James A. Fellows Yates	24dc2a2cec	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-11-03 10:03:07 +01:00
James Fellows Yates	d487a1ff2f	Addd FASTP adadapter list	2022-11-02 12:39:34 +01:00
Sofia Stamouli	e4307ad8ab	Change modules.config to include porechop_porechop	2022-11-01 20:50:42 +01:00
Sofia Stamouli	3faea8aac5	Fix porechop conflict	2022-11-01 17:34:37 +01:00
Mahwash Jamy	aecf308840	Update documentation for krakenuniq	2022-10-31 16:41:35 +00:00
Mahwash Jamy	851016e497	Update nextflow_scheme.json	2022-10-31 16:17:40 +00:00
Mahwash Jamy	febcbfc057	add missing parameters to nextflow.config	2022-10-31 16:07:53 +00:00