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Author	SHA1	Message	Date
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 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
James Fellows Yates	52907dcc26	Prettier	2023-01-31 13:07:07 +01:00
James A. Fellows Yates	d49344cefd	Merge pull request #228 from nf-core/bt2-error ... Fix channel structure when supplying own host bt2 index	2023-01-31 13:03:53 +01:00
James Fellows Yates	225773000f	Fix channel structure when supplying own host bt2 index	2023-01-31 12:00:48 +01:00
James A. Fellows Yates	43a503096e	Merge pull request #227 from nf-core/mqc-update [skip ci] ... Tweak MultiQC config [skip ci]	2023-01-31 11:11:52 +01:00
James Fellows Yates	01fca90496	Tweak MultiQC config [skip ci]	2023-01-31 11:08:46 +01:00
James A. Fellows Yates	b4d01ac226	Formatting tweaks	2023-01-31 10:23:36 +01:00
James A. Fellows Yates	f47c294931	Merge pull request #186 from genomic-medicine-sweden/update_output ... Start the documentation of output.md	2023-01-31 09:58:54 +01:00
sofstam	366745bdbe	Prettier in usage	2023-01-31 09:38:43 +01:00
sofstam	5b738ad353	Review + prettier	2023-01-31 09:35:40 +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
sofstam	0edef9ea57	Review suggestions + prettier	2023-01-30 11:16:18 +01:00
sofstam	bc2876228c	Apply review suggestions	2023-01-25 15:11:43 +01:00
James Fellows Yates	a77a437313	Triple patch combo!	2023-01-25 15:02:02 +01:00
James Fellows Yates	f63cec3473	Actually patch the patch	2023-01-25 14:58:19 +01:00
James Fellows Yates	d761edb615	Patch the patch	2023-01-25 14:55:57 +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	2cbb56194a	Merge pull request #224 from nf-core/revert-metaphlan-nanopore-filter [skip ci] ... Remove metaphlan3 nanopore filter as _sometimes_ it can work	2023-01-25 13:48:29 +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
sofstam	4f8ac72e1f	Add description of each tool	2023-01-25 13:25:33 +01:00
Sofia Stamouli	5d12785ca4	Merge branch 'nf-core:dev' into update_output	2023-01-25 09:47:30 +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 Fellows Yates	7843665544	Link rather than mv	2023-01-24 15:32:49 +01:00
James A. Fellows Yates	c765b3f0bc	Merge branch 'dev' into allow-targz-motus	2023-01-24 15:20:29 +01:00
James Fellows Yates	f940b07dfe	Remove changes from other PR	2023-01-24 15:15:02 +01:00
James Fellows Yates	bdbb111344	Turn off all profilers in generla stats	2023-01-24 15:08:28 +01:00
James Fellows Yates	a993300099	Tweaks to MultiQC based on full test experiments	2023-01-24 15:06:42 +01:00
Moritz E. Beber	2431bddcbc	Merge pull request #222 from nf-core/fix-save-minimap2 ... fix: correct pattern to publish minimap2 index	2023-01-24 14:57:46 +01:00
James Fellows Yates	e7d7affcd0	Pick up Kraken2 files correctly	2023-01-24 14:44:14 +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
Moritz E. Beber	40f1e7b27a	fix: correct pattern to publish minimap2 index	2023-01-24 14:15:51 +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