265 commits

Author	SHA1	Message	Date
sofstam	2456038567	Merge branch 'dev' into add_taxpasta_merge	2023-02-16 15:07:51 +01:00
sofstam	de6a4214ef	Add taxpasta_merge to taxprofiler	2023-02-16 14:29:52 +01:00
James Fellows Yates	7dfcdd015b	Re-add the 'native' combined kaiju output	2023-02-16 14:02:13 +01:00
James Fellows Yates	79b4db9a34	Move kaiju2table to profiling	2023-02-16 13:39:05 +01:00
James A. Fellows Yates	45ac6fedc2	Merge pull request #237 from nf-core/bracken-params ... Support Kraken and Bracken db_params in database sheet	2023-02-09 10:59:27 +01:00
James A. Fellows Yates	70eb84b8d5	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2023-02-09 08:01:52 +01:00
James Fellows Yates	b3837cce5b	Relax strictness so can supply empty db_params but block if only single parameter with out ;	2023-02-08 15:44:37 +01:00
James Fellows Yates	fe3d42ffd7	Make bracken db_params be a semi-colon separate list to allow kraken and bracken parameters	2023-02-08 13:34:36 +01:00
James Fellows Yates	18886c0cbc	Start trying a different method with maps in profiling	2023-02-07 15:51:25 +01:00
James Fellows Yates	059cd17114	Fix exporting of mapped/unmapped reads for consistency across both short and long reads	2023-02-07 11:43:40 +01:00
James A. Fellows Yates	47efd193cb	Merge pull request #219 from nf-core/allow-targz-motus [skip ci] ... Allow all tool's databases to be provided as `.tar.gz` files	2023-01-25 13:48:43 +01:00
James A. Fellows Yates	4289e1f901	Remove metaphlan3 nanopore filter as _sometimes_ it can work	2023-01-24 15:42:14 +01:00
James A. Fellows Yates	c765b3f0bc	Merge branch 'dev' into allow-targz-motus	2023-01-24 15:20:29 +01:00
James A. Fellows Yates	00178d3431	Merge pull request #221 from nf-core/metaphlan3-filter-nanopore ... Filter out nanopore data prior Metaphlan3	2023-01-24 14:39:02 +01:00
James Fellows Yates	14826d5205	Separate conditions, remove some left-over dumps	2023-01-24 13:20:58 +01:00
James Fellows Yates	0358489be0	Remove metaphlan profiling for nanopore as it appears to always result in 100% unclassified	2023-01-24 13:05:52 +01:00
James A. Fellows Yates	6eafcc6499	Try Moritz's trick, assuming validate_db_rows already checks for tool name validity	2023-01-24 12:43:34 +01:00
James Fellows Yates	4df3409f4a	Merge branch 'dev' of github.com:nf-core/taxprofiler into allow-targz-motus	2023-01-24 11:50:28 +01:00
James Fellows Yates	9205831273	Start adding filter for long read and MP3	2023-01-24 11:50:10 +01:00
James Fellows Yates	1a148c5d49	Remove double If and format for readability	2023-01-24 10:48:23 +01:00
James A. Fellows Yates	d56e3133f9	Allow databases of all tools to arrive as tar.gz	2023-01-24 10:45:01 +01:00
James Fellows Yates	606ffc0eb1	Remove platform specificity for MALT	2023-01-20 13:40:59 +01:00
James Fellows Yates	e5c6db96c8	update all modules to make templaite compatible	2022-12-23 17:23:05 +01:00
Sofia Stamouli	41c1ae9d1a	Commit suggestion ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-12-23 12:20:37 +01:00
sofstam	85906ab1cb	Optional untar on dbs	2022-12-23 11:25:57 +01:00
James A. Fellows Yates	25bb4304e8	Merge pull request #187 from nf-core/revert-pep ... Revert PEP validation back to python samplesheet check	2022-12-20 15:03:18 +01:00
James Fellows Yates	577da7e835	Remove .first() as the module only executes once anyway and we get a ugly warning	2022-12-20 13:59:14 +01:00
James Fellows Yates	11db981a88	minor fixes	2022-12-20 13:55:15 +01:00
James A. Fellows Yates	7709245874	Update subworkflows/local/input_check.nf ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-20 13:54:05 +01:00
James A. Fellows Yates	578081df2e	Merge pull request #189 from nf-core/database-check ... Adds (native groovy!) database check	2022-12-13 08:43:00 +01:00
James Fellows Yates	7c66968fef	More comments	2022-12-12 11:04:21 +01:00
James Fellows Yates	460f3ca157	Add database sheet validation	2022-12-12 11:03:40 +01:00
James Fellows Yates	07bd989bc6	Start work on groovy native datbase checks	2022-12-12 10:02:22 +01:00
James Fellows Yates	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +01:00
James Fellows Yates	8939ce3e20	Start adding bracken/combinebrackenreports (need smodule update)	2022-12-11 16:52:34 +01:00
Moritz E. Beber	24e5bc5410	refactor: use shorter and more explicit syntax	2022-12-04 21:54:10 +01:00
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +01:00
James Fellows Yates	0dccfddc24	Switch order back	2022-12-03 21:38:25 +01:00
James A. Fellows Yates	cf8ad96771	Update subworkflows/local/profiling.nf	2022-12-02 15:09:08 +01:00
James Fellows Yates	ab42f6b662	wteak message	2022-12-02 12:49:00 +01:00
James Fellows Yates	a3cd188b1f	Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test	2022-12-02 12:48:18 +01:00
James Fellows Yates	de74e4f727	Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md	2022-12-02 12:47:14 +01:00
James A. Fellows Yates	a34b240dfc	Merge pull request #174 from nf-core/malt-update ... Update MALT	2022-12-01 13:58:30 +01:00
James A. Fellows Yates	4f6eb6fd75	Merge pull request #153 from mjamy/add-krakenuniq-module ... Add krakenuniq module	2022-12-01 09:03:29 +01:00
James Fellows Yates	d7fbe55849	Add KU to the test profiles and add id to KU processes	2022-11-29 14:19:01 +01:00
Moritz E. Beber	ddcf38de22	refactor: make mappings explicit	2022-11-29 10:14:20 +01:00
James Fellows Yates	9feb6c2db6	Update MALT	2022-11-24 14:44:04 +01:00
sofstam	481f90589c	Apply review suggestions	2022-11-23 09:08:22 +01:00
sofstam	30af26a8b3	Include the mapped reads in samtools stats	2022-11-22 16:50:50 +01:00
James Fellows Yates	06659af777	Remove flatten	2022-11-22 13:36:40 +01:00