180 commits

Author	SHA1	Message	Date
sofstam	896a39e68d	Apply review suggestions	2022-12-12 13:19:59 +01:00
sofstam	c9a6320dac	Merge branch 'update_output' of https://github.com/genomic-medicine-sweden/taxprofiler into update_output ... Conflicts: docs/output.md	2022-12-12 09:13:02 +01:00
James Fellows Yates	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +01:00
sofstam	b35d26744d	Add classifiers	2022-12-09 17:11:48 +01:00
Sofia Stamouli	6d0b5d0a58	Prettier	2022-12-09 15:38:59 +01:00
Sofia Stamouli	98f3ab9fd1	Apply prettier	2022-12-09 15:35:51 +01:00
sofstam	c5f4c9486a	Start the documentation of output.md	2022-12-09 15:30:11 +01:00
Sofia Stamouli	a622dcaef0	Delete one line	2022-12-09 13:59:37 +01:00
sofstam	5373c58331	Merge branch 'dev' into update_usage	2022-12-09 13:05:42 +01:00
sofstam	97fbc2bceb	Update usage.md	2022-12-09 12:58:51 +01:00
sofstam	3af71d9c63	Merge branch 'dev' into update_usage	2022-12-09 10:35:12 +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
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +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
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	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 Fellows Yates	6459d8920f	Linting!	2022-11-03 14:05:43 +01:00
Mahwash Jamy	aecf308840	Update documentation for krakenuniq	2022-10-31 16:41:35 +00:00
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
Sofia Stamouli	8c3e80b6ea	Add helptest to nextflow_schema,add versions to longread_preprocessing	2022-10-25 11:13:26 +02:00
nf-core-bot	00038db634	[automated] Fix linting with Prettier	2022-10-25 08:51:58 +00:00
Moritz E. Beber	ca7dc308cb	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-10-21 16:36:35 +02:00
Moritz E. Beber	7bd6112133	docs: describe Bracken database usage	2022-10-21 10:18:11 +02:00
Sofia Stamouli	0481bb9449	Prettier	2022-10-18 17:48:40 +02:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
James A. Fellows Yates	4f27998852	Update usage.md	2022-10-14 14:37:52 +02:00
Sofia Stamouli	e98cd038c7	[skip ci] ... Add description for MALT	2022-10-12 12:56:54 +02:00
Sofia Stamouli	0b16010b92	Add tutorials section	2022-10-12 11:39:03 +02:00
Sofia Stamouli	d09a8e0545	[skip ci]	2022-10-11 17:44:48 +02:00
Sofia Stamouli	17b2ad3199	Add prettier	2022-10-11 17:29:41 +02:00
Sofia Stamouli	f22cf0c921	Update usage.md	2022-10-11 16:41:44 +02:00
Sofia Stamouli	2423c9d87c	Add headers	2022-10-11 15:02:01 +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
Rafal Stepien	768f9980d8	Add pep_input_base_dir to workflow. Just need to update modules	2022-09-15 12:31:49 -04:00
Rafal Stepien	5f3eee9a4a	Add working version of PEP-nf-core integration	2022-09-14 14:28:48 -04:00
Sofia Stamouli	ded6d7ab1f	Update docs/usage.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-13 18:13:00 +02:00
Sofia Stamouli	0072c29a6f	Update docs/usage.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-13 18:12:14 +02:00
Sofia Stamouli	c664508240	Update usage.md	2022-09-13 15:56:06 +02:00
James Fellows Yates	3a6536b149	Add tube map properly	2022-09-07 11:22:22 +02:00
James Fellows Yates	3eb136ec3c	Merge branch 'dev' into json-schema	2022-08-31 12:55:49 +02:00
James A. Fellows Yates	28d8d3f8fb	Merge branch 'dev' into nf-core-template-merge-2.5	2022-08-31 09:16:34 +02:00
James Fellows Yates	0107330d92	Clarify specifying output parameters in database db_params column	2022-08-31 08:34:57 +02:00
James Fellows Yates	bdcae4f934	More docs and tweat to usage.md	2022-08-30 16:04:05 +02:00
nf-core-bot	6dfca81761	Template update for nf-core/tools version 2.5	2022-08-30 13:43:03 +00:00
James Fellows Yates	33a5402b25	Add emitting porechop logs to multiqc and fix collection of others	2022-07-19 13:50:39 +02:00
James A. Fellows Yates	26e31c782d	Merge branch 'dev' into motus	2022-07-04 13:14:42 +02:00
James Fellows Yates	4552b53e75	Add note about MALT version to docs	2022-06-20 08:30:23 +02:00
James Fellows Yates	6c6f5e0913	Merge branch 'dev' of github.com:nf-core/taxprofiler into dev	2022-06-09 08:21:51 +02:00
James Fellows Yates	ec13b8d608	Remove support for uncompressed FASTQ files	2022-06-09 08:21:48 +02:00
James A. Fellows Yates	dc48935651	Apply suggestions from code review	2022-06-07 20:19:45 +02:00
JIANHONG OU	c8a59adbce	remove the database auto-download for mOTUs.	2022-06-03 14:13:58 -04:00
James A. Fellows Yates	53c4399052	Merge branch 'dev' into motus	2022-06-02 21:38:35 +02:00
James A. Fellows Yates	a196e0f628	Merge branch 'dev' into add-filtlong	2022-06-02 11:51:26 +02:00
JIANHONG OU	4d77b47e8d	create a new test profile config for mOTUs.	2022-05-31 08:47:38 -04:00
James Fellows Yates	310ac6b450	Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong	2022-05-31 13:05:52 +02:00
James Fellows Yates	77da358e87	Separate dark and light mode logos, add to README and add to MQC report	2022-05-31 12:45:38 +02:00
ZandraFagernas	74b48f0919	Add files via upload	2022-05-28 13:29:24 +02:00
James A. Fellows Yates	d67543503b	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-05-07 13:15:21 +02:00
James Fellows Yates	47a5ae0cff	Add FASTP complexity option	2022-05-07 06:09:05 +02:00
Lauri Mesilaakso	02517733aa	Update docs/usage.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-05-06 10:40:59 +02:00
ljmesi	6618e8cac6	Change param to a more generic name	2022-05-05 13:20:34 +02:00
ljmesi	557d31dfd2	Add parameter for turning on longread host removal	2022-05-05 13:19:10 +02:00
James Fellows Yates	031cb45934	Add initial longread QC filtering - requires filtlong module update	2022-05-01 07:18:14 +02:00
James Fellows Yates	a4a9b161d8	Lintin	2022-04-29 22:02:44 +02:00
James Fellows Yates	8126d16dee	Add draft version of DIAMOND	2022-04-29 21:59:42 +02:00
Sofia Stamouli	236141f065	Resolve conflicts with dev	2022-04-20 10:17:10 +02:00
James A. Fellows Yates	ac714dd30f	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-20 09:22:10 +02:00
sofstam	1b7ff2265d	Update usage.md, reformat test.config and modules.config	2022-04-19 13:04:58 +02:00
James Fellows Yates	457c13e8b7	Add additional tips for host removal	2022-04-17 17:55:23 +02:00
James Fellows Yates	818d3bd053	Complete documentation for preprocessing subworkflows	2022-04-17 17:53:22 +02:00
James A. Fellows Yates	b8b11fd065	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-11 10:30:29 +02:00
James Fellows Yates	b892fd0be5	Initial attempt at docs	2022-04-10 22:17:44 +02:00
James A. Fellows Yates	edce6603ef	Merge branch 'dev' into nf-core-template-merge-2.3.2	2022-03-24 14:10:58 +01:00
nf-core-bot	6b939e6728	Template update for nf-core/tools version 2.3.1	2022-03-23 13:57:56 +00:00
ljmesi	2e1b6c5d0a	Add info on Nanopore reads to fastq_1 column	2022-03-18 11:00:36 +01:00
nf-core-bot	699d26b149	Template update for nf-core/tools version 2.3	2022-03-15 21:05:37 +00:00
James Fellows Yates	12e7b428f2	initial template build from nf-core/tools, version 2.2	2022-02-18 07:55:14 +01:00