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Author	SHA1	Message	Date
James Fellows Yates	5c549e5ce3	Remove TODOs and references to under development	2023-03-02 13:49:03 +01:00
James Fellows Yates	a14937f668	Remove unused module and fix module structure for samplesheet_check	2023-03-02 13:34:10 +01:00
Sofia Stamouli	d9f687667e	Merge pull request #249 from genomic-medicine-sweden/update_taxpasta ... Update taxpasta	2023-03-02 08:53:38 +01:00
sofstam	7ae7fb528b	Prettier	2023-03-01 22:17:07 +01:00
sofstam	58f09ed659	Update taxpasta/merge module	2023-03-01 22:12:09 +01:00
Sofia Stamouli	b93c7082b8	Merge pull request #248 from genomic-medicine-sweden/update_taxpasta_merge ... Update taxpasta/merge to version 0.2.0 and add taxonomy argument	2023-02-27 15:19:58 +01:00
Sofia Stamouli	df5303270d	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 14:18:30 +01:00
Sofia Stamouli	fff7453d0c	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 14:18:22 +01:00
Sofia Stamouli	9621d34c4a	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 14:18:11 +01:00
Sofia Stamouli	54af021965	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 14:18:01 +01:00
sofstam	99fe8adb1b	Add helptext	2023-02-27 13:49:02 +01:00
sofstam	c94bfb0cf1	Fix prettier	2023-02-27 13:09:07 +01:00
sofstam	4dea308c22	Linting	2023-02-27 11:34:19 +01:00
Sofia Stamouli	69430ef851	Update nextflow.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 11:02:55 +01:00
Sofia Stamouli	e3e465df1f	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 11:00:59 +01:00
Sofia Stamouli	d454ceed86	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 11:00:42 +01:00
Sofia Stamouli	1aef73cda8	Update docs/output.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 10:39:44 +01:00
Sofia Stamouli	d96e0a17a5	Update conf/modules.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 10:39:10 +01:00
sofstam	489650feb8	Linting	2023-02-27 10:24:14 +01:00
sofstam	2f0c68a833	Last review suggestions	2023-02-27 10:15:42 +01:00
sofstam	78d7001bea	Document the taxonomy parameters	2023-02-24 16:53:49 +01:00
sofstam	a7ae57c94e	Fix linting	2023-02-24 15:53:54 +01:00
sofstam	e18e68faa5	Apply review suggestion	2023-02-24 15:50:24 +01:00
sofstam	5dc3cbc278	Rename taxonomy argument	2023-02-24 13:04:38 +01:00
sofstam	5a6fcf1f42	Update taxpasta/merge to version 0.2.0 and add taxonomy argument	2023-02-24 11:44:07 +01:00
James A. Fellows Yates	78c2d275e6	Merge pull request #245 from nf-core/ku-docs [skip ci] ... Fix typo in schema docs [skip ci]	2023-02-23 14:35:54 +01:00
James Fellows Yates	cd4614f387	Fix typo in schema docs [skip ci]	2023-02-23 14:00:00 +01:00
James A. Fellows Yates	91255b4d2d	Merge pull request #244 from nf-core/taxpasta-ku-fix ... Fix KrakenUniq Taxpasta issue	2023-02-22 14:20:06 +01:00
James A. Fellows Yates	32c0d8d6a5	Fix KrakenUniq Taxpasta issue	2023-02-22 08:24:48 +01:00
James A. Fellows Yates	877f6ca8b3	Merge pull request #243 from nf-core/rma2info-label-fix ... Fix label base.config for MEGAN_RMA2INFO	2023-02-20 21:46:32 +01:00
James A. Fellows Yates	3d1659dac7	Merge pull request #242 from genomic-medicine-sweden/minor_fixes ... Remove standardised_tables	2023-02-20 20:43:09 +01:00
James A. Fellows Yates	9847b8d9a7	Fix label base.config for MEGAN_RMA2INFO	2023-02-20 20:35:22 +01:00
sofstam	90aa7551a9	Fix the motus_versions	2023-02-20 14:27:57 +01:00
sofstam	3fa1b0c17d	Remove standardised_tables	2023-02-20 13:48:04 +01:00
Sofia Stamouli	599c8d3592	Merge pull request #241 from genomic-medicine-sweden/add_taxpasta_merge ... Add taxpasta_merge to taxprofiler	2023-02-20 13:15:30 +01:00
sofstam	04bc978ef6	Remove taxonomy parameter from taxpasta	2023-02-20 11:56:06 +01:00
sofstam	211b5f3a68	Apply review suggestions	2023-02-20 11:49:31 +01:00
sofstam	90a5668007	run_malt false in test and add text in output.md	2023-02-17 15:38:36 +01:00
sofstam	f0aa89cb87	Rename taxpasta parameters and remove samplesheet parameter	2023-02-17 14:47:29 +01:00
sofstam	604df56fdb	Add a description about the files used by taxpasta	2023-02-17 13:49:13 +01:00
sofstam	08bfa6a1a7	Apply review suggestions for docs	2023-02-17 13:43:38 +01:00
sofstam	5ebc22dd29	Add icon in nextflow_schema.json	2023-02-17 12:58:33 +01:00
sofstam	27b7171b96	Apply review suggestions	2023-02-17 09:16:58 +01:00
sofstam	c9b521234b	Prettier for docs	2023-02-16 16:38:00 +01:00
sofstam	dad64a688d	Add documentation for taxpasta module	2023-02-16 16:33:36 +01:00
sofstam	25d44c955e	Merge dev into add_taxpasta_merge	2023-02-16 15:16:05 +01:00
sofstam	2456038567	Merge branch 'dev' into add_taxpasta_merge	2023-02-16 15:07:51 +01:00
James A. Fellows Yates	bb3c49389f	Merge pull request #240 from nf-core/move-kaiju2table ... Move kaiju2table to profiling	2023-02-16 15:03:59 +01:00
sofstam	de6a4214ef	Add taxpasta_merge to taxprofiler	2023-02-16 14:29:52 +01:00
James Fellows Yates	7dfcdd015b	Re-add the 'native' combined kaiju output	2023-02-16 14:02:13 +01:00