677 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James Fellows Yates	577da7e835	Remove .first() as the module only executes once anyway and we get a ugly warning	2022-12-20 13:59:14 +01:00
James A. Fellows Yates	41063bc670	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-20 13:56:01 +01:00
James Fellows Yates	11db981a88	minor fixes	2022-12-20 13:55:15 +01:00
James A. Fellows Yates	7709245874	Update subworkflows/local/input_check.nf ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-20 13:54:05 +01:00
James Fellows Yates	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +01:00
James A. Fellows Yates	13c4f44ca6	Merge pull request #185 from nf-core/nf-core-template-merge-2.7.1 ... Important! Template update for nf-core/tools v2.7.1	2022-12-09 12:58:28 +01:00
James Fellows Yates	dca0b86c78	Fix versions	2022-12-09 10:28:48 +01:00
James Fellows Yates	da3d2d96e6	Fix linting	2022-12-09 10:27:50 +01:00
James Fellows Yates	1ccd0a0767	Merge branch 'dev' into nf-core-template-merge-2.7.1	2022-12-09 10:16:17 +01:00
nf-core-bot	36f3b5723b	Template update for nf-core/tools version 2.7.1	2022-12-08 13:18:23 +00:00
James A. Fellows Yates	1687b43596	Merge pull request #183 from nf-core/update-bracken-params ... Update bracken so parameters come directly from database args	2022-12-07 16:39:52 +01:00
James Fellows Yates	d8751787ac	Update bracken so parameters come directly from database args	2022-12-07 07:27:40 +01:00
James Fellows Yates	3dba6405c5	Sets correct default for --shortread_qc_mergepairs	2022-12-06 11:47:16 +01:00
Moritz E. Beber	9064584356	Merge pull request #180 from nf-core/rename-exclude-unmerged ... refactor: change parameter exclude unmerged to include	2022-12-05 10:53:32 +01:00
Moritz E. Beber	24e5bc5410	refactor: use shorter and more explicit syntax	2022-12-04 21:54:10 +01:00
Moritz E. Beber	b2088bcbb3	docs: improve description of shortread_qc_includeunmerged	2022-12-04 21:53:38 +01:00
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +01:00
James A. Fellows Yates	7992edd181	Merge pull request #181 from nf-core/sep-krakenuniq-test ... Filter out Nanopore reads from Bracken	2022-12-04 13:57:11 +01:00
James Fellows Yates	0a0dffa37c	Try separating MALT	2022-12-04 12:06:33 +01:00
James Fellows Yates	0dccfddc24	Switch order back	2022-12-03 21:38:25 +01:00
James A. Fellows Yates	cf8ad96771	Update subworkflows/local/profiling.nf	2022-12-02 15:09:08 +01:00
James Fellows Yates	ab42f6b662	wteak message	2022-12-02 12:49:00 +01:00
James Fellows Yates	a3cd188b1f	Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test	2022-12-02 12:48:18 +01:00
James Fellows Yates	de74e4f727	Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md	2022-12-02 12:47:14 +01:00
Sofia Stamouli	c56c6ea694	Merge pull request #176 from nf-core/update_motus ... Include NCBI taxid, read counts and mgc arguments in motus	2022-12-02 12:18:58 +01:00
Sofia Stamouli	7e7299203c	Set values to false	2022-12-02 08:55:23 +01:00
sofstam	6d140c683a	Merge branch 'dev' into update_motus	2022-12-01 18:49:23 +01:00
James A. Fellows Yates	80c25008d0	Merge pull request #177 from nf-core/sep-krakenuniq-test ... Separate KrakenUniq test run	2022-12-01 17:34:30 +01:00
nf-core-bot	410196c37b	[automated] Fix linting with Prettier	2022-12-01 14:33:34 +00:00
sofstam	4800a5f03e	Update schema	2022-12-01 14:23:40 +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 Fellows Yates	f960c14caf	Fix typos	2022-12-01 13:46:57 +01:00
sofstam	38a818fd17	Apply review suggestions	2022-12-01 13:42:21 +01:00
James A. Fellows Yates	ef1d2da179	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-01 12:53:34 +01:00
sofstam	1965ade961	Update schema	2022-12-01 11:32:51 +01:00
sofstam	e5bb627402	Apply review suggestions	2022-12-01 11:12:31 +01:00
James Fellows Yates	bc98f5b80f	Separate KrakenUniq test run	2022-12-01 10:37:14 +01:00
nf-core-bot	8067012c01	[automated] Fix linting with Prettier	2022-12-01 09:15:35 +00:00
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
sofstam	933b820c19	Apply review suggestions	2022-11-29 16:57:07 +01:00
Sofia Stamouli	e85c75dcba	Merge branch 'dev' into update_motus	2022-11-29 15:12:31 +01:00
sofstam	12dd836e9c	Fix conflict	2022-11-29 15:00:27 +01:00
sofstam	f389029848	Fix merge conflic	2022-11-29 14:38:39 +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
Sofia Stamouli	7e3ece53bd	Update modules.config	2022-11-29 13:31:00 +01:00
Sofia Stamouli	0088b07220	Fix trailing whitespace	2022-11-29 13:28:04 +01:00
James A. Fellows Yates	770a35d7ac	Update conf/modules.config	2022-11-29 12:49:20 +01:00
Sofia Stamouli	ba727a81ae	Fix left-padding spaces	2022-11-29 12:45:14 +01:00
Sofia Stamouli	71b52b9c94	Apply review suggestions	2022-11-29 11:58:23 +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