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Author	SHA1	Message	Date
Rafal Stepien	00aa94a403	Merge branch 'add-pep-support' of github.com:nf-core/taxprofiler into nf-core-add-pep-support	2022-09-28 14:51:13 -04:00
Rafal Stepien	bfd260e9c8	Update workflows/taxprofiler.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-28 12:40:43 -04:00
James Fellows Yates	87edc4569c	Move to a function	2022-09-27 15:46:17 +02:00
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	1584d6fc51	Update workflows/taxprofiler.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-19 10:43:04 -04:00
Rafal Stepien	0ccbf50938	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-19 09:49:37 -04:00
Rafal Stepien	5b6c18f0a2	Update nextflow.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-19 09:49:28 -04:00
Rafal Stepien	e84b64f7e1	Update modules/local/samplesheet_check.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-19 09:49:20 -04:00
James A. Fellows Yates	187946ec80	Merge pull request #136 from nf-core/metaphlan3/mergemetaphlantables ... Add MetaPhlAn3 per-database multi-sample taxon tables	2022-09-19 13:45:50 +02:00
Rafal Stepien	9349346864	Remove --pep parameter and leave just --input	2022-09-16 10:14:01 -04:00
James A. Fellows Yates	016efcb807	Merge branch 'dev' into metaphlan3/mergemetaphlantables	2022-09-16 16:02:38 +02:00
James A. Fellows Yates	a2a9f458ec	Merge pull request #137 from nf-core/motus-merge-meta ... Standardise mOTUs table merge	2022-09-16 16:01:38 +02:00
James A. Fellows Yates	f43c54317c	Update subworkflows/local/standardisation_profiles.nf ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2022-09-16 15:20:47 +02:00
James Fellows Yates	63b3cc678f	Merge branch 'motus-merge-meta' of github.com:nf-core/taxprofiler into motus-merge-meta	2022-09-16 10:25:28 +02:00
James Fellows Yates	c5cc21d29e	Update motus merge module to remove unused channel	2022-09-16 10:25:24 +02:00
James A. Fellows Yates	2c83b367a7	Apply suggestions from code review	2022-09-16 09:28:42 +02:00
James Fellows Yates	4e7857e2ed	Standardise mOTUs table merge	2022-09-16 08:36:34 +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
James A. Fellows Yates	cdb21d17b3	Merge branch 'dev' into metaphlan3/mergemetaphlantables	2022-09-15 13:08:57 +02:00
James A. Fellows Yates	d9795a4fdc	Merge pull request #130 from nf-core/krakentools/combinekreports ... Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU	2022-09-15 13:00:07 +02:00
James Fellows Yates	19a195ed14	Append profiler to resulting file	2022-09-15 12:30:39 +02:00
James Fellows Yates	21ae9d85c3	Ensure merge metaphlan3 tables happens on per database basis	2022-09-15 12:29:54 +02:00
James A. Fellows Yates	cd83c04c98	Merge pull request #135 from nf-core/dev-warning ... Update README.md	2022-09-15 08:30:41 +02:00
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 A. Fellows Yates	5414ae2e55	Apply suggestions from code review	2022-09-14 11:20:40 +02:00
James Fellows Yates	abbbf9c7ab	Update to use tar module compatible for our test databases	2022-09-14 11:16:28 +02:00
Sofia Stamouli	343a9e8d16	Merge pull request #131 from nf-core/FAQs_README ... Update usage.md	2022-09-14 09:00:17 +02:00
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
James Fellows Yates	05e9d92444	Add centrigue kreports	2022-09-13 16:47:19 +02:00
Sofia Stamouli	c664508240	Update usage.md	2022-09-13 15:56:06 +02:00
James Fellows Yates	c8dbf5be47	Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU	2022-09-13 15:47:28 +02:00
James A. Fellows Yates	db688575f6	Merge pull request #128 from nf-core/fastp-patch-removal ... use proper working FASTP module	2022-09-09 19:07:12 +02:00
James Fellows Yates	a764bc4807	Start works - need updated module though t have meta	2022-09-09 13:57:06 +02:00
James A. Fellows Yates	b28052f1ec	Remove patch from modules.json	2022-09-09 11:15:25 +02:00
James Fellows Yates	f087136ec9	use proper working FASTP module	2022-09-09 11:12:47 +02:00
James A. Fellows Yates	3fc7f1f0f8	Merge pull request #127 from nf-core/module-update ... Update all modules	2022-09-08 16:23:44 +02:00
James Fellows Yates	60224e9149	Patch fastp until I have an OK on the module update	2022-09-08 14:25:23 +02:00
James A. Fellows Yates	cc5df924e4	Merge branch 'dev' into module-update	2022-09-08 13:36:21 +02:00
James A. Fellows Yates	74c164bbcd	Merge pull request #126 from nf-core/kaiju2table-move ... Kaiju2table move	2022-09-08 13:21:27 +02:00
James Fellows Yates	fc26948950	Fix MultiQC	2022-09-08 12:49:38 +02:00
James Fellows Yates	d11257b330	Module update	2022-09-08 08:08:36 +02:00
James Fellows Yates	bbd8049ca1	Remove duplicated multqic mixing	2022-09-07 13:44:08 +02:00
James A. Fellows Yates	6f87c681fd	Merge pull request #125 from nf-core/workflow-tube-map ... Workflow tube map	2022-09-07 12:52:38 +02:00
James Fellows Yates	832d981976	Don't have per sample directory as unnecessary if file names are unique with the db in them	2022-09-07 12:22:17 +02:00
James Fellows Yates	3a6536b149	Add tube map properly	2022-09-07 11:22:22 +02:00
James Fellows Yates	175be0075a	Add tube map	2022-09-07 11:22:06 +02:00
James Fellows Yates	7c5f9d0c24	Start work on more merging tools	2022-09-06 17:34:45 +02:00
James A. Fellows Yates	8c6f88d1b5	Merge pull request #118 from nf-core/motus-test-fix ... Fix mOTUs CI and old param warn	2022-09-05 10:38:58 +02:00