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966 commits 7 branches 0 tags 7.5 MiB
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40 commits

Author SHA1 Message Date
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