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Author	SHA1	Message	Date
James Fellows Yates	02c06b9f7b	Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file	2022-06-30 18:33:11 +02:00
James Fellows Yates	27f174d17e	Merge remote-tracking branch 'origin/dev' into malt-to-krona	2022-06-30 12:01:33 +02:00
James Fellows Yates	0050f45345	Add taxonomy directory param	2022-06-30 11:43:52 +02:00
James A. Fellows Yates	913080a5b1	Merge pull request #96 from MillironX/feature/kaiju2krona ... Add Krona output for Kaiju profiles	2022-06-29 09:27:25 +02:00
Thomas A. Christensen II	6673ccf8d8	Update channel assignment alignment in profiling subworkflow ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-06-28 09:00:43 -05:00
Thomas A. Christensen II	069370db86	Add unclassified and verbose flags to kaiju2krona	2022-06-28 09:00:42 -05:00
Thomas A. Christensen II	4de43040a3	Switch to using raw classifications for Kaiju2Krona	2022-06-28 09:00:41 -05:00
James Fellows Yates	af854f5f34	Update mimetype for database csv as per https://github.com/nf-core/mag/pull/325/files	2022-06-28 12:42:41 +02:00
James A. Fellows Yates	e66c2b9b87	Merge pull request #94 from MillironX/feature/centrifuge2krona ... Add Krona output for Centrifuge profiles	2022-06-27 17:13:31 +02:00
James A. Fellows Yates	5e554a3a0b	Merge pull request #91 from MillironX/feature/kreport2krona ... Add Krona output for Kraken classification	2022-06-27 16:55:55 +02:00
Thomas A. Christensen II	821dd844d8	Add Kaiju profile conversion to visualization workflow	2022-06-27 09:23:20 -05:00
Thomas A. Christensen II	5b80c7cab9	Install KAIJU_KAIJU2KRONA	2022-06-27 08:58:28 -05:00
Thomas A. Christensen II	23fec89b06	Add Krona chart creation for Centrifuge reports	2022-06-27 08:52:29 -05:00
Thomas A. Christensen II	18284e6e32	Add run_krona option to allow skipping Krona chart creation	2022-06-27 08:45:08 -05:00
Thomas A. Christensen II	15ac8b39fa	Add citation for Krona	2022-06-27 08:25:48 -05:00
Thomas A. Christensen II	0e8edd5b2f	Add output configuration for Kraken Krona chart	2022-06-27 08:25:47 -05:00
Thomas A. Christensen II	ad9bc4b7e9	Add the visualization workflow to the main workflow	2022-06-27 08:25:38 -05:00
Thomas A. Christensen II	a40a442178	Create VISUALIZATION_KRONA workflow to create Krona charts	2022-06-27 08:22:47 -05:00
James A. Fellows Yates	a83f53f64c	Merge pull request #93 from nf-core/malt-rollback ... MALT version rollback	2022-06-20 09:43:09 +02:00
James Fellows Yates	4552b53e75	Add note about MALT version to docs	2022-06-20 08:30:23 +02:00
James Fellows Yates	4ff2145e44	Roll back MALT version	2022-06-20 08:23:14 +02:00
James A. Fellows Yates	2e7f26f380	Replace header tuple with sub-set list of only relevant columns for sample checking	2022-06-14 20:09:48 +00:00
Thomas A. Christensen II	5da8d5b741	Install KRONA_KTIMPORTTEXT	2022-06-14 10:34:34 -05:00
Thomas A. Christensen II	87678c127b	Add KRONA_CLEANUP process module	2022-06-14 10:34:33 -05:00
Thomas A. Christensen II	a84f693479	Install KRAKENTOOLS_KREPORT2KRONA module	2022-06-14 08:13:36 -05:00
James Fellows Yates	c1a7d6335f	Do not require fixed column order	2022-06-13 21:02:12 +02:00
James A. Fellows Yates	3dcda7446b	Merge pull request #86 from nf-core/support-aligned-reads ... Add working read alignment output for MALT/Kraken2/Centrifuge/DIAMOND	2022-06-13 11:23:34 +02:00
James Fellows Yates	e0ad49ebc9	Fix metadata manipulaton for malt	2022-06-10 19:33:37 +02:00
James A. Fellows Yates	621b6a3d09	Add comments about MALT id replacement and refactor for simplicity	2022-06-10 11:27:51 +02:00
James Fellows Yates	6c6f5e0913	Merge branch 'dev' of github.com:nf-core/taxprofiler into dev	2022-06-09 08:21:51 +02:00
James Fellows Yates	ec13b8d608	Remove support for uncompressed FASTQ files	2022-06-09 08:21:48 +02:00
James Fellows Yates	800c0dd2aa	Merge branch 'support-aligned-reads' of github.com:nf-core/taxprofiler into support-aligned-reads	2022-06-09 08:16:01 +02:00
James Fellows Yates	490a8a8a84	Remove dump	2022-06-09 08:15:58 +02:00
James A. Fellows Yates	dc48935651	Apply suggestions from code review	2022-06-07 20:19:45 +02:00
James A. Fellows Yates	ebdd5683b2	Apply suggestions from code review	2022-06-03 22:33:48 +02:00
James Fellows Yates	9462032d00	Fix MALT save_alignemnts reads and some clean up	2022-06-03 22:29:04 +02:00
JIANHONG OU	713a341e09	clean up ci.yml	2022-06-03 15:22:33 -04:00
JIANHONG OU	9fa6ecad56	debug for database csv file	2022-06-03 14:50:03 -04:00
JIANHONG OU	3cd3d2dad3	prettier write .	2022-06-03 14:38:59 -04:00
JIANHONG OU	22f65eedc7	fix the download address for downloadDB for mOTUs.	2022-06-03 14:16:25 -04:00
JIANHONG OU	c8a59adbce	remove the database auto-download for mOTUs.	2022-06-03 14:13:58 -04:00
James Fellows Yates	d48b3be5a7	Tweak DIAMOND save_reads message	2022-06-03 13:55:17 +02:00
James Fellows Yates	3313b90453	Fix JSOn schema	2022-06-03 13:50:48 +02:00
James A. Fellows Yates	96fecb2bfc	Merge branch 'dev' into support-aligned-reads	2022-06-03 13:48:54 +02:00
James A. Fellows Yates	53c4399052	Merge branch 'dev' into motus	2022-06-02 21:38:35 +02:00
James A. Fellows Yates	43ea8d299c	Merge pull request #74 from nf-core/add-filtlong ... Add initial longread QC filtering - requires filtlong module update	2022-06-02 20:10:46 +02:00
James Fellows Yates	2838c136bd	Prettier	2022-06-02 12:51:39 +02:00
James A. Fellows Yates	c9581b1796	Merge branch 'dev' into support-aligned-reads	2022-06-02 12:45:29 +02:00
James Fellows Yates	d3d28da1b1	Update after review	2022-06-02 11:53:53 +02:00
James A. Fellows Yates	a196e0f628	Merge branch 'dev' into add-filtlong	2022-06-02 11:51:26 +02:00