988 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James Fellows Yates	8ca9fad3b1	move errorStrategy to config	2023-03-07 11:09:25 +01:00
James Fellows Yates	b5a2983c5f	Make modules entries consistent	2023-03-07 11:06:35 +01:00
Sofia Stamouli	d647e61a2f	Merge pull request #253 from nf-core/futher-further-prerelease-updates ... Futher further prerelease updates: FALCO display in MultiQC	2023-03-06 15:56:50 +01:00
James Fellows Yates	2d9dede6d4	Improve python regex	2023-03-06 12:59:08 +01:00
James Fellows Yates	6e64c2b5a9	Fix copy paste error	2023-03-06 10:50:36 +01:00
James Fellows Yates	735212c9ee	Fix the non-updated KAIJU2TABLE name	2023-03-06 10:47:36 +01:00
James Fellows Yates	a2a1b9cbf0	Phrasing tweak	2023-03-06 10:42:30 +01:00
James Fellows Yates	4938549d65	Clarify some documentation	2023-03-06 10:41:32 +01:00
James Fellows Yates	9ed384e0f2	Collapse FALCO and FASTQC sections, move FALCO/FASTQC sections together	2023-03-06 10:37:09 +01:00
James Fellows Yates	1f1c63bb51	Start fixing FastQC/Falco display in MultiQC	2023-03-06 09:47:26 +01:00
James Fellows Yates	a5138ed6e0	Fix ugly warn when KAIJU2TABLE not run	2023-03-06 08:17:50 +01:00
James A. Fellows Yates	f0f89eb082	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 14:58:21 +01:00
James A. Fellows Yates	c66c67524c	Update nextflow.config ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 13:33:41 +01:00
James A. Fellows Yates	799a44cb8c	Merge pull request #252 from nf-core/further-prerelease-changes ... Further prerelease changes	2023-03-03 10:16:23 +01:00
James Fellows Yates	6d9cdd3c78	And the other file	2023-03-03 09:15:21 +01:00
James Fellows Yates	5feebf8d69	Fix linting issues	2023-03-03 09:12:11 +01:00
James Fellows Yates	74a5343524	Add taxpasta to tubemap	2023-03-03 09:11:10 +01:00
James A. Fellows Yates	6c2ce4a1c9	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 08:37:31 +01:00
James A. Fellows Yates	0c9d6cabe8	Merge pull request #250 from nf-core/pre-release-updates ... Cleanup PR for release	2023-03-02 13:54:45 +01:00
James Fellows Yates	ec89187504	Update CHANGELOG for first release	2023-03-02 13:53:32 +01:00
James Fellows Yates	aedf0b34de	Bump version for release	2023-03-02 13:51:28 +01:00
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