355 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James A. Fellows Yates	c215ed5607	Merge branch 'dev' into motus/merge	2022-07-15 10:52:42 +02:00
James A. Fellows Yates	cc3967a3fd	Apply suggestions from code review	2022-07-15 10:51:41 +02:00
James A. Fellows Yates	d7ca3df160	Merge pull request #104 from nf-core/motus-profile-update ... Update mOTUs profile module and mix log for multiqc	2022-07-14 16:03:01 +02:00
James Fellows Yates	449b6a5553	Fix file name output clashing wiht multiqc	2022-07-13 15:25:58 +02:00
James Fellows Yates	31119f83c2	Send to MQC only the log file not the meta	2022-07-13 14:29:47 +02:00
James Fellows Yates	13280e2468	Fix .empty	2022-07-13 12:44:44 +02:00
James Fellows Yates	eaa69b65d8	Update mOTUs profile module and mix log for multiqc	2022-07-13 12:38:30 +02:00
James Fellows Yates	c22946cfab	Fix motu versions not being exported if not run	2022-07-13 12:36:29 +02:00
James Fellows Yates	d8c0e9e7fe	Prettier	2022-07-12 11:41:07 +02:00
James Fellows Yates	a0ee82bf43	Add motus/merge and biom support	2022-07-12 11:39:26 +02:00
James A. Fellows Yates	8082c7d108	Merge pull request #97 from nf-core/malt-to-krona ... Add Krona support for MALT	2022-07-05 15:17:52 +02:00
James A. Fellows Yates	1eba859bf8	Merge pull request #82 from jianhong/motus ... add motus profile.	2022-07-04 14:16:12 +02:00
James A. Fellows Yates	26e31c782d	Merge branch 'dev' into motus	2022-07-04 13:14:42 +02:00
James Fellows Yates	447b8f0905	Get fixed Krona module and add Krona taxonomy to test profile	2022-07-01 17:21:19 +02:00
James Fellows Yates	97e6cdf4b4	Add Krona taxonomy DB to schema build	2022-06-30 18:36:13 +02:00
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
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 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