42 commits

Author	SHA1	Message	Date
James Fellows Yates	5c549e5ce3	Remove TODOs and references to under development	2023-03-02 13:49:03 +01:00
James A. Fellows Yates	c4e366d47d	Add full test data and documentation of the test data	2023-02-02 11:59:26 +01:00
James A. Fellows Yates	b34a021db7	Specify the difference between classification/profiling	2023-01-16 14:43:46 +01:00
James Fellows Yates	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +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
Sofia Stamouli	696edfb866	Apply prettier	2022-11-04 12:05:23 +01:00
Sofia Stamouli	79dd3930bb	Add samtools to README	2022-11-03 16:52:01 +01:00
Sofia Stamouli	511cb16a61	Apply review suggestions	2022-10-20 16:55:57 +02:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
Sofia Stamouli	bd56bc0ed6	Add minimap2 and update contributors	2022-10-12 11:10:53 +02:00
Sofia Stamouli	35b7fc26f7	[skip ci]	2022-10-11 17:01:08 +02:00
Sofia Stamouli	f24344c168	Update README.md	2022-10-11 16:30:42 +02:00
Sofia Stamouli	dea45c66c2	Add Krona description	2022-10-11 14:59:48 +02:00
Sofia Stamouli	58dffc0c5d	Add KrakenUniq and Filtlong in documentation	2022-10-11 12:36:48 +02:00
James A. Fellows Yates	3ca9058b9c	Merge pull request #133 from rafalstepien/add-pep-support ... Add working version of PEP-nf-core integration	2022-09-30 10:21:15 +02:00
Rafal Stepien	9349346864	Remove --pep parameter and leave just --input	2022-09-16 10:14:01 -04:00
Rafal Stepien	768f9980d8	Add pep_input_base_dir to workflow. Just need to update modules	2022-09-15 12:31:49 -04:00
James A. Fellows Yates	23a33a63cc	Update README.md	2022-09-15 08:11:37 +02:00
Rafal Stepien	5f3eee9a4a	Add working version of PEP-nf-core integration	2022-09-14 14:28:48 -04:00
James Fellows Yates	175be0075a	Add tube map	2022-09-07 11:22:06 +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
nf-core-bot	6dfca81761	Template update for nf-core/tools version 2.5	2022-08-30 13:43:03 +00:00
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
Moritz E. Beber	a9fbe47992	Merge branch 'dev' into nf-core-template-merge-2.4	2022-05-19 08:42:28 +02:00
nf-core-bot	a560492353	Template update for nf-core/tools version 2.4	2022-05-16 10:22:38 +00:00
sofstam	6736a2a980	Update README.md, nextflow_schema.json	2022-04-13 19:00:52 +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	fafb7e0f6f	Update README.md	2022-03-24 16:59:12 +01:00
James Fellows Yates	203cd2e7d3	Prettier	2022-03-24 14:31:53 +01:00
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	4940ec57ff	Remove unnecessary extra point	2022-03-21 18:26:26 +01:00
ljmesi	24a01529f5	Add mentioning about Nanopore reads pre-processing	2022-03-18 15:47:46 +01:00
James A. Fellows Yates	424f11f5ed	Update README.md	2022-03-17 13:16:16 +01:00
James A. Fellows Yates	ac77676d2b	Merge branch 'dev' into nf-core-template-merge-2.3	2022-03-17 13:11:34 +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	cf55cc592c	Get skeleton read processing to input for profiling	2022-02-18 16:51:01 +01:00
James Fellows Yates	7321daf4f6	Update README with approximate pipeline outline	2022-02-18 08:41:34 +01:00
James Fellows Yates	12e7b428f2	initial template build from nf-core/tools, version 2.2	2022-02-18 07:55:14 +01:00