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Author	SHA1	Message	Date
Moritz E. Beber	fd8a0df2a6	refactor: add warning when run_kraken2 is missing	2022-10-17 17:16:21 +02:00
Moritz E. Beber	563b34c9c3	refactor: rename process to kraken2	2022-10-14 14:48:27 +02:00
Moritz E. Beber	95621ebd8a	fix: include local module	2022-10-14 14:47:08 +02:00
James A. Fellows Yates	4f27998852	Update usage.md	2022-10-14 14:37:52 +02:00
Moritz E. Beber	9dc819ceff	style: reformat schema	2022-10-14 13:16:54 +02:00
Moritz E. Beber	c4f6468275	chore: update parameters schema	2022-10-14 12:55:26 +02:00
Moritz E. Beber	7f8180f458	fix: emit tool versions	2022-10-14 12:49:07 +02:00
Moritz E. Beber	767663d975	chore: add Bracken to test configs	2022-10-14 12:18:55 +02:00
Moritz E. Beber	ca38d002de	feat: integrate Bracken into the profiling pipeline	2022-10-14 12:18:07 +02:00
Moritz E. Beber	4f728648f5	feat: add process to standardize kraken report	2022-10-14 10:56:14 +02:00
Moritz E. Beber	4352d35937	chore: install Bracken module	2022-10-14 10:52:17 +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	4e771ab2c7	Merge pull request #142 from genomic-medicine-sweden/update_readme ... Add KrakenUniq and Filtlong in documentation	2022-10-12 11:38:01 +02:00
Sofia Stamouli	bd56bc0ed6	Add minimap2 and update contributors	2022-10-12 11:10:53 +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	35b7fc26f7	[skip ci]	2022-10-11 17:01:08 +02:00
Sofia Stamouli	f22cf0c921	Update usage.md	2022-10-11 16:41:44 +02:00
Sofia Stamouli	f24344c168	Update README.md	2022-10-11 16:30:42 +02:00
Sofia Stamouli	2423c9d87c	Add headers	2022-10-11 15:02:01 +02:00
Sofia Stamouli	dea45c66c2	Add Krona description	2022-10-11 14:59:48 +02:00
James A. Fellows Yates	f25ee17fcf	Merge pull request #141 from nf-core/minimap-patch ... Remove necessity of patch	2022-10-11 12:46:26 +02:00
James Fellows Yates	56bae85755	Remove necessity of patch	2022-10-11 12:38:18 +02:00
Sofia Stamouli	58dffc0c5d	Add KrakenUniq and Filtlong in documentation	2022-10-11 12:36:48 +02:00
James A. Fellows Yates	ff1670169a	Merge pull request #138 from nf-core/nf-core-template-merge-2.6 ... Important! Template update for nf-core/tools v2.6	2022-10-06 13:03:45 +02:00
Moritz E. Beber	5f3dbd28de	fix: patch inputs to correspond to previous version	2022-10-05 13:51:15 +02:00
Moritz E. Beber	180cac0395	fix: adapt to new samtools/view input	2022-10-05 13:49:35 +02:00
Moritz E. Beber	f5af9fd939	fix: adjust import paths to re-organization	2022-10-05 13:40:43 +02:00
Moritz E. Beber	b407fbcdce	chore: force update all modules	2022-10-05 12:24:18 +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	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
James A. Fellows Yates	44146b8fe3	Apply suggestions from code review	2022-09-30 08:34:53 +02:00
James A. Fellows Yates	8b559fba86	Pin version to get NXF to download correctly	2022-09-29 13:31:02 -04:00
Rafal Stepien	04d28e6520	Merge branch 'nf-core-add-pep-support' into add-pep-support	2022-09-28 14:51:38 -04:00
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