42 commits

Author	SHA1	Message	Date
James Fellows Yates	87fd5f72d0	Fix template	2023-05-02 13:20:09 +02:00
James Fellows Yates	1eb951715f	MultiQC optimisations for DIAMOND and Falco	2023-04-20 15:57:57 +02:00
James Fellows Yates	e92196cd12	Remove left over comment	2023-03-07 11:10:10 +01:00
James Fellows Yates	2d9dede6d4	Improve python regex	2023-03-06 12:59:08 +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	5feebf8d69	Fix linting issues	2023-03-03 09:12:11 +01:00
James Fellows Yates	01fca90496	Tweak MultiQC config [skip ci]	2023-01-31 11:08:46 +01:00
James Fellows Yates	bdbb111344	Turn off all profilers in generla stats	2023-01-24 15:08:28 +01:00
James Fellows Yates	a993300099	Tweaks to MultiQC based on full test experiments	2023-01-24 15:06:42 +01:00
James Fellows Yates	92dff9b453	Standardise file names using only underscore	2023-01-17 10:58:30 +01:00
James Fellows Yates	480248bcfd	Deactivate all classifer columns from general stats	2023-01-17 10:33:35 +01:00
James Fellows Yates	0947e9b8ca	Fix mOTUs issues	2023-01-16 15:09:30 +01:00
James Fellows Yates	d6fa45b500	update MultiQC and include latest modules	2023-01-16 14:39:52 +01:00
James A. Fellows Yates	25bb4304e8	Merge pull request #187 from nf-core/revert-pep ... Revert PEP validation back to python samplesheet check	2022-12-20 15:03:18 +01:00
Sofia Stamouli	07a1cfae62	Update assets/multiqc_config.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-16 11:46:42 +01:00
Sofia Stamouli	5a592f086e	Update assets/multiqc_config.yml ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-16 11:46:35 +01:00
Sofia Stamouli	a2c81e33fd	Prettier	2022-12-16 08:38:58 +01:00
Sofia Stamouli	d6db04503e	Configuration of multiqc report	2022-12-15 17:04:45 +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	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	1bd6dbfe58	Add samtools stats for long-reads	2022-10-28 11:40:50 +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
James A. Fellows Yates	8b559fba86	Pin version to get NXF to download correctly	2022-09-29 13:31:02 -04:00
James Fellows Yates	43a8aa4405	Remove detect_reads.py and replace remaining checks with nextflow code instead	2022-09-27 15:32:51 +02:00
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
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	a97bb69cd2	Prettier	2022-08-23 14:24:57 +02:00
James Fellows Yates	25bcc0798d	Start work on multiQC config with distinguishing Kraken/Centrifuge	2022-07-27 14:40:17 +02:00
nf-core-bot	a3bcf8665a	[automated] Fix linting with Prettier	2022-07-26 18:47:40 +00:00
James A. Fellows Yates	65ae82efc4	Define separte krakena nd centrigfue modules	2022-07-26 18:37:33 +00:00
James A. Fellows Yates	e76b299705	Start working getting kraken and centrifuge working in MQC	2022-07-26 08:18:54 +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
James Fellows Yates	b892fd0be5	Initial attempt at docs	2022-04-10 22:17:44 +02:00
nf-core-bot	6b939e6728	Template update for nf-core/tools version 2.3.1	2022-03-23 13:57:56 +00:00
James Fellows Yates	12e7b428f2	initial template build from nf-core/tools, version 2.2	2022-02-18 07:55:14 +01:00