232 commits

Author	SHA1	Message	Date
James Fellows Yates	8ca9fad3b1	move errorStrategy to config	2023-03-07 11:09:25 +01:00
James Fellows Yates	b5a2983c5f	Make modules entries consistent	2023-03-07 11:06:35 +01:00
James Fellows Yates	a5138ed6e0	Fix ugly warn when KAIJU2TABLE not run	2023-03-06 08:17:50 +01:00
James A. Fellows Yates	6c2ce4a1c9	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 08:37:31 +01:00
James Fellows Yates	5c549e5ce3	Remove TODOs and references to under development	2023-03-02 13:49:03 +01:00
Sofia Stamouli	d96e0a17a5	Update conf/modules.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 10:39:10 +01:00
sofstam	2f0c68a833	Last review suggestions	2023-02-27 10:15:42 +01:00
sofstam	a7ae57c94e	Fix linting	2023-02-24 15:53:54 +01:00
sofstam	e18e68faa5	Apply review suggestion	2023-02-24 15:50:24 +01:00
sofstam	5dc3cbc278	Rename taxonomy argument	2023-02-24 13:04:38 +01:00
sofstam	5a6fcf1f42	Update taxpasta/merge to version 0.2.0 and add taxonomy argument	2023-02-24 11:44:07 +01:00
James A. Fellows Yates	9847b8d9a7	Fix label base.config for MEGAN_RMA2INFO	2023-02-20 20:35:22 +01:00
sofstam	04bc978ef6	Remove taxonomy parameter from taxpasta	2023-02-20 11:56:06 +01:00
sofstam	90a5668007	run_malt false in test and add text in output.md	2023-02-17 15:38:36 +01:00
sofstam	f0aa89cb87	Rename taxpasta parameters and remove samplesheet parameter	2023-02-17 14:47:29 +01:00
sofstam	27b7171b96	Apply review suggestions	2023-02-17 09:16:58 +01:00
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 Fellows Yates	ce1118930d	Resource optimisation	2023-02-09 13:33:39 +01:00
James Fellows Yates	cc7d219267	Revert "optimisation for single-cpu processes" ... This reverts commit a731669b8e.	2023-02-09 13:32:29 +01:00
James Fellows Yates	a731669b8e	optimisation for single-cpu processes	2023-02-09 13:31:57 +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	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
sofstam	5363274867	Add some last documentation	2023-02-02 13:58:48 +01:00
James Fellows Yates	7ce55a99e8	Fix linting	2023-02-02 13:08:16 +01:00
James A. Fellows Yates	c4e366d47d	Add full test data and documentation of the test data	2023-02-02 11:59:26 +01:00
James A. Fellows Yates	1d7da61801	Merge pull request #223 from nf-core/multiqc-tweaks ... MultiQC Tweaks after full-test experiments	2023-01-30 11:25:28 +01:00
James A. Fellows Yates	098ec087c9	Merge pull request #217 from nf-core/combine-kreports-fix [skip ci] ... Dont fail on divide by 0 errors on centrifuge	2023-01-25 13:48:06 +01:00
James Fellows Yates	a993300099	Tweaks to MultiQC based on full test experiments	2023-01-24 15:06:42 +01:00
James Fellows Yates	e7d7affcd0	Pick up Kraken2 files correctly	2023-01-24 14:44:14 +01:00
Moritz E. Beber	40f1e7b27a	fix: correct pattern to publish minimap2 index	2023-01-24 14:15:51 +01:00
James Fellows Yates	1c820f21b3	Dont fail on divide by 0 errors on centrifuge	2023-01-20 17:53:55 +01:00
James A. Fellows Yates	d9003924be	Merge pull request #201 from genomic-medicine-sweden/removo_todo ... Remove TODOs from test configs	2023-01-19 13:15:14 +01:00
James Fellows Yates	92dff9b453	Standardise file names using only underscore	2023-01-17 10:58:30 +01:00
James Fellows Yates	c8f6d713a3	Add tool names to end of prefix files for easier distinguishing in general stats	2023-01-16 14:49:44 +01:00
James Fellows Yates	d6fa45b500	update MultiQC and include latest modules	2023-01-16 14:39:52 +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
Sofia Stamouli	c23eb968f9	Remove TODOs from test configs	2022-12-16 15:20:06 +01:00
James Fellows Yates	9e6a91aff9	Distinguish Kraken2 from Bracken	2022-12-15 13:25:01 +01:00
James Fellows Yates	3b86a22556	Fix falco publication names	2022-12-15 12:57:49 +01:00
James Fellows Yates	88589fbc53	Fix publishing of log files of rpreprocessing steps	2022-12-15 10:35:06 +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	3df0a383da	Update combine bracken outputs to include meta for publishing purposes	2022-12-12 10:10:24 +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