577 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
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
James A. Fellows Yates	dfcaaae1fb	Merge pull request #83 from ZandraFagernas/dev ... Uploaded logo	2022-06-02 11:31:32 +02:00
James Fellows Yates	fa70a413cb	Use finally working filtlong module	2022-05-31 21:12:09 +02:00
James Fellows Yates	16ec5bf74a	Update parameter names	2022-05-31 20:11:19 +02:00
JIANHONG OU	f0eb88cbe2	add mOTUs to modules.config	2022-05-31 08:57:00 -04:00
JIANHONG OU	4d77b47e8d	create a new test profile config for mOTUs.	2022-05-31 08:47:38 -04:00
JIANHONG OU	e916c91de3	Delete null/pipeline_info directory	2022-05-31 07:57:15 -04:00
JIANHONG OU	7191ad7a9b	Merge branch 'nf-core:dev' into motus	2022-05-31 07:56:56 -04:00
James Fellows Yates	792e2d019b	Fix merge error in schema	2022-05-31 13:06:48 +02:00
James Fellows Yates	310ac6b450	Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong	2022-05-31 13:05:52 +02:00
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
ZandraFagernas	74b48f0919	Add files via upload	2022-05-28 13:29:24 +02:00
JIANHONG OU	f14141574e	fix the end line issue for modules.json	2022-05-25 08:03:23 -04:00
JIANHONG OU	4b3216c1cb	filter fasta inputs for mOTUs; ... fix the typo for nopreprocessing in nextflow.config.	2022-05-24 08:42:18 -04:00
JIANHONG OU	68d0cc00fa	add motus profile.	2022-05-23 08:05:06 -04:00
James A. Fellows Yates	ba75685550	Merge pull request #81 from nf-core/nf-core-template-merge-2.4 ... Important! Template update for nf-core/tools v2.4	2022-05-19 11:00:48 +01:00