891 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James Fellows Yates	cd4614f387	Fix typo in schema docs [skip ci]	2023-02-23 14:00:00 +01:00
James A. Fellows Yates	91255b4d2d	Merge pull request #244 from nf-core/taxpasta-ku-fix ... Fix KrakenUniq Taxpasta issue	2023-02-22 14:20:06 +01:00
James A. Fellows Yates	32c0d8d6a5	Fix KrakenUniq Taxpasta issue	2023-02-22 08:24:48 +01:00
James A. Fellows Yates	877f6ca8b3	Merge pull request #243 from nf-core/rma2info-label-fix ... Fix label base.config for MEGAN_RMA2INFO	2023-02-20 21:46:32 +01:00
James A. Fellows Yates	3d1659dac7	Merge pull request #242 from genomic-medicine-sweden/minor_fixes ... Remove standardised_tables	2023-02-20 20:43:09 +01:00
James A. Fellows Yates	9847b8d9a7	Fix label base.config for MEGAN_RMA2INFO	2023-02-20 20:35:22 +01:00
sofstam	90aa7551a9	Fix the motus_versions	2023-02-20 14:27:57 +01:00
sofstam	3fa1b0c17d	Remove standardised_tables	2023-02-20 13:48:04 +01:00
Sofia Stamouli	599c8d3592	Merge pull request #241 from genomic-medicine-sweden/add_taxpasta_merge ... Add taxpasta_merge to taxprofiler	2023-02-20 13:15:30 +01:00
sofstam	04bc978ef6	Remove taxonomy parameter from taxpasta	2023-02-20 11:56:06 +01:00
sofstam	211b5f3a68	Apply review suggestions	2023-02-20 11:49:31 +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	604df56fdb	Add a description about the files used by taxpasta	2023-02-17 13:49:13 +01:00
sofstam	08bfa6a1a7	Apply review suggestions for docs	2023-02-17 13:43:38 +01:00
sofstam	5ebc22dd29	Add icon in nextflow_schema.json	2023-02-17 12:58:33 +01:00
sofstam	27b7171b96	Apply review suggestions	2023-02-17 09:16:58 +01:00
sofstam	c9b521234b	Prettier for docs	2023-02-16 16:38:00 +01:00
sofstam	dad64a688d	Add documentation for taxpasta module	2023-02-16 16:33:36 +01:00
sofstam	25d44c955e	Merge dev into add_taxpasta_merge	2023-02-16 15:16:05 +01:00
sofstam	2456038567	Merge branch 'dev' into add_taxpasta_merge	2023-02-16 15:07:51 +01:00
James A. Fellows Yates	bb3c49389f	Merge pull request #240 from nf-core/move-kaiju2table ... Move kaiju2table to profiling	2023-02-16 15:03:59 +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 A. Fellows Yates	4e818efe6d	Update docs/output.md ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-02-16 13:45:04 +01:00
James Fellows Yates	79b4db9a34	Move kaiju2table to profiling	2023-02-16 13:39:05 +01:00
James A. Fellows Yates	21d9135b14	Merge pull request #238 from nf-core/process-optmisations ... Resource optimisation	2023-02-09 15:41:30 +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	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 A. Fellows Yates	31d05d1994	Merge pull request #236 from nf-core/mapped-bam-fixes ... Fix exporting of mapped/unmapped reads for consistency across both short and long reads	2023-02-07 18:42:18 +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	de5bdc36c5	Merge pull request #230 from genomic-medicine-sweden/documentation ... Add documentation	2023-02-03 16:34:09 +01:00
sofstam	4123e06981	Apply last review suggestions	2023-02-03 15:54:29 +01:00
sofstam	3e2b181182	Apply review suggestions	2023-02-03 15:42:45 +01:00
Sofia Stamouli	ffc884b542	Merge branch 'nf-core:dev' into documentation	2023-02-03 15:22:51 +01:00
James A. Fellows Yates	2b40d809d8	Merge pull request #231 from nf-core/docs-t [skip ci] ... Add warning about database parameters [skip ci]	2023-02-03 10:14:38 +01:00
James A. Fellows Yates	b4f88a29ce	Update docs/usage.md [skip ci]	2023-02-03 09:46:01 +01:00
James A. Fellows Yates	11a8624b39	Add warning about database parameters [skip ci]	2023-02-03 09:42:20 +01:00
sofstam	5363274867	Add some last documentation	2023-02-02 13:58:48 +01:00
James A. Fellows Yates	2e925e5b11	Merge pull request #229 from nf-core/full-test-profile-docs ... Add full test data and documentation of the test data	2023-02-02 13:10:39 +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	a6b4e3c4d4	Merge pull request #225 from nf-core/output-docs-imporvements ... Output Formatting tweaks	2023-01-31 13:25:07 +01:00
James Fellows Yates	932dc12fb1	Add list of expected tools in MultiQC report [skip ci]	2023-01-31 13:09:53 +01:00