160 commits

Author	SHA1	Message	Date
Sofia Stamouli	7b1a53b062	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-10-25 11:19:08 +02:00
Sofia Stamouli	8c3e80b6ea	Add helptest to nextflow_schema,add versions to longread_preprocessing	2022-10-25 11:13:26 +02:00
Sofia Stamouli	19231538da	Prettier	2022-10-20 16:59:32 +02:00
Sofia Stamouli	511cb16a61	Apply review suggestions	2022-10-20 16:55:57 +02:00
Sofia Stamouli	0481bb9449	Prettier	2022-10-18 17:48:40 +02:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
Moritz E. Beber	9dc819ceff	style: reformat schema	2022-10-14 13:16:54 +02:00
Moritz E. Beber	c4f6468275	chore: update parameters schema	2022-10-14 12:55:26 +02:00
Moritz E. Beber	fdb8a7f740	Merge branch 'devel' into nf-core-template-merge-2.6	2022-10-05 12:21:54 +02:00
nf-core-bot	51bacb00e6	Template update for nf-core/tools version 2.6	2022-10-05 03:30:53 +00:00
Rafal Stepien	bfd260e9c8	Update workflows/taxprofiler.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-28 12:40:43 -04:00
Rafal Stepien	0ccbf50938	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-19 09:49:37 -04:00
Rafal Stepien	9349346864	Remove --pep parameter and leave just --input	2022-09-16 10:14:01 -04:00
Rafal Stepien	5f3eee9a4a	Add working version of PEP-nf-core integration	2022-09-14 14:28:48 -04:00
James Fellows Yates	806208c4b1	Final tweaks to schema, and add a couple of notes for dev guidance on where their various --save_reads parameters are injected	2022-08-31 08:30:26 +02:00
James Fellows Yates	acd0570b4a	Finalise first pass of nextflow json documentation	2022-08-31 07:56:39 +02:00
James Fellows Yates	bdcae4f934	More docs and tweat to usage.md	2022-08-30 16:04:05 +02:00
James Fellows Yates	c2eaa3f6b0	Prettier	2022-08-30 14:33:40 +02:00
James Fellows Yates	d19a473c59	Merge branch 'filtlong-in-tests' into json-schema	2022-08-30 14:33:19 +02:00
James Fellows Yates	8917e29e35	Fix accidental overly zelous search-and-replace	2022-08-30 14:11:48 +02:00
James Fellows Yates	3f8f32cba8	Make longread quality ftilering opt out	2022-08-30 14:08:05 +02:00
James Fellows Yates	2cc07183a0	Standardise QC parameter system and turn on both porechop/filtlong in tests	2022-08-30 13:58:58 +02:00
James Fellows Yates	d4af88e3ff	Make kaiju parameter clearer for documentation purpses and update documentation	2022-08-25 15:50:28 +02:00
James Fellows Yates	d6d51e0e43	Start work on reordering json schema parameters	2022-08-24 15:23:51 +02:00
James Fellows Yates	d8c0e9e7fe	Prettier	2022-07-12 11:41:07 +02:00
James Fellows Yates	a0ee82bf43	Add motus/merge and biom support	2022-07-12 11:39:26 +02:00
James A. Fellows Yates	8082c7d108	Merge pull request #97 from nf-core/malt-to-krona ... Add Krona support for MALT	2022-07-05 15:17:52 +02:00
James A. Fellows Yates	26e31c782d	Merge branch 'dev' into motus	2022-07-04 13:14:42 +02:00
James Fellows Yates	97e6cdf4b4	Add Krona taxonomy DB to schema build	2022-06-30 18:36:13 +02:00
James Fellows Yates	af854f5f34	Update mimetype for database csv as per https://github.com/nf-core/mag/pull/325/files	2022-06-28 12:42:41 +02:00
Thomas A. Christensen II	18284e6e32	Add run_krona option to allow skipping Krona chart creation	2022-06-27 08:45:08 -05:00
JIANHONG OU	c8a59adbce	remove the database auto-download for mOTUs.	2022-06-03 14:13:58 -04:00
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 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 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
JIANHONG OU	68d0cc00fa	add motus profile.	2022-05-23 08:05:06 -04:00
James Fellows Yates	0f651873dd	Linting	2022-05-07 06:12:24 +02:00
James Fellows Yates	47a5ae0cff	Add FASTP complexity option	2022-05-07 06:09:05 +02:00
James Fellows Yates	87a1d80519	Add working output for Kraken2/Centrifuge/DIAMOND	2022-05-07 05:22:35 +02:00
ljmesi	6618e8cac6	Change param to a more generic name	2022-05-05 13:20:34 +02:00
ljmesi	557d31dfd2	Add parameter for turning on longread host removal	2022-05-05 13:19:10 +02:00
ljmesi	d94534e8ac	Simplify params which control host removal publish	2022-05-05 09:07:33 +02:00
ljmesi	c833d4fd9a	Fix issues found with prettier	2022-05-03 11:42:05 +02:00
ljmesi	17039ebc6b	Fix type to boolean for flags	2022-05-03 11:07:23 +02:00
ljmesi	fa1c132635	Update nextflow_schema	2022-05-03 11:03:25 +02:00
James Fellows Yates	031cb45934	Add initial longread QC filtering - requires filtlong module update	2022-05-01 07:18:14 +02:00
James Fellows Yates	a4a9b161d8	Lintin	2022-04-29 22:02:44 +02:00
James Fellows Yates	8126d16dee	Add draft version of DIAMOND	2022-04-29 21:59:42 +02:00
Sofia Stamouli	194b89e66a	Prettier	2022-04-26 12:53:39 +02:00
Sofia Stamouli	7afda265c5	Enumerating taxon	2022-04-26 11:27:18 +02:00
Sofia Stamouli	f4480feb9b	Prettier	2022-04-25 17:45:26 +02:00
sofstam	d082d67bcb	Add kaiju2table to taxprofiler	2022-04-25 17:36:29 +02:00
James A. Fellows Yates	cd3c8f6a89	Merge branch 'dev' into hostremoval-publish-fix	2022-04-21 11:43:06 +02:00
Sofia Stamouli	236141f065	Resolve conflicts with dev	2022-04-20 10:17:10 +02:00
James A. Fellows Yates	d16cd75652	Merge branch 'dev' into hostremoval-publish-fix	2022-04-20 09:53:51 +02:00
Sofia Stamouli	4e1b1269be	Apply prettier	2022-04-19 13:11:43 +02:00
James Fellows Yates	b036ed5b73	Prettier	2022-04-17 22:28:18 +02:00
James Fellows Yates	2cfcdf2dd2	Add finer controler over for hostremoval saving	2022-04-17 22:27:04 +02:00
James Fellows Yates	cc73cdd51d	Add generation of taxon-table like output for MALT	2022-04-16 07:42:30 +02:00
sofstam	0e5c9e7bdd	Type:boolean for kaiju in nextflow_schema.json	2022-04-14 09:14:05 +02:00
sofstam	6736a2a980	Update README.md, nextflow_schema.json	2022-04-13 19:00:52 +02:00
James Fellows Yates	aa2d07c42a	Fix merge cockup	2022-04-13 14:19:19 +02:00
James A. Fellows Yates	70f94603b0	Merge branch 'dev' into hostremoval	2022-04-13 13:59:51 +02:00
James Fellows Yates	dfeaa0d1fe	Rename subworkflow parameters for consistency	2022-04-13 12:00:28 +02:00
James A. Fellows Yates	967b1f7d6e	Merge branch 'dev' into run-merging	2022-04-12 09:28:10 +02:00
James A. Fellows Yates	025083061e	Merge branch 'dev' into hostremoval	2022-04-11 13:36:03 +02:00
James Fellows Yates	a634814d84	Formatting and fix fastp output	2022-04-08 13:34:00 +02:00
James Fellows Yates	ca011ccc5b	Fix cat_fastq naming logic?	2022-04-08 13:28:37 +02:00
Sofia Stamouli	3d45ac57ae	Prettier	2022-04-07 16:42:22 +02:00
sofstam	26779a4420	Remove db_name from nextflow.config	2022-04-07 16:27:19 +02:00
sofstam	606e5da7d5	Check if PR works with centrifuge/centrifuge module	2022-04-07 16:13:17 +02:00
James A. Fellows Yates	b554aa3e4d	Merge branch 'dev' into hostremoval	2022-04-07 14:00:10 +02:00
Moritz E. Beber	7ab3aa546b	refactor: use flags to publish reads	2022-04-06 10:27:11 +02:00
James Fellows Yates	d46ddd972c	Expand tests and fix schema after review	2022-04-05 11:04:30 +02:00
James Fellows Yates	bb6dd738bd	Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk	2022-04-04 21:21:34 +02:00
James Fellows Yates	613f6a5565	Prettier	2022-04-04 21:21:29 +02:00
James A. Fellows Yates	3d662d2e06	Merge branch 'dev' into complexity-filter-bbduk	2022-04-04 21:19:36 +02:00
James Fellows Yates	a384162810	Add prinseq as alternative complexity filtering	2022-04-04 21:16:51 +02:00
sofstam	3a56206513	Centrifuge classification	2022-04-04 16:55:48 +02:00
sofstam	d897c922b2	Add centrifuge classificatioN	2022-04-04 13:51:51 +02:00
James A. Fellows Yates	b2e29ea23a	Merge branch 'dev' into hostremoval	2022-04-03 17:24:07 +02:00
James Fellows Yates	066ceb2bca	Remove flagstat as bowtie2 reports this itself	2022-04-03 17:23:14 +02:00
James Fellows Yates	b055df5ea0	Add bbduk complexity (entropy-based) filtering	2022-04-02 17:02:05 +02:00
Moritz E. Beber	e579f9f5f3	style: apply prettier	2022-04-02 14:59:44 +02:00
Moritz E. Beber	fb9afa013a	fix: add metaphlan parameter to schema	2022-04-02 14:59:44 +02:00
James Fellows Yates	dcda815bfb	Add final adapterremoval options to match fastp functionality	2022-04-01 09:50:08 +02:00
James Fellows Yates	c4c93bd59d	Start working on adding adapterremoval	2022-03-31 15:31:45 +02:00
James Fellows Yates	76e9624e3f	NOW commit the adapte rtrim flag	2022-03-30 11:31:37 +02:00
Sofia Stamouli	c552819c72	Apply prettier again	2022-03-28 22:15:31 +02:00
sofstam	d25f97c506	Prettier format	2022-03-28 22:08:05 +02:00
sofstam	0e0e8128e8	Prettier format	2022-03-28 13:53:16 +02:00
sofstam	59d3f18a75	Update nextflow_schema.json	2022-03-25 17:18:04 +01:00
sofstam	37a70dc3e3	Merge branch 'dev' into classification_centrifuge	2022-03-25 16:18:35 +01:00
James Fellows Yates	dfcf8f7b1a	Prettier	2022-03-25 15:10:52 +01:00
James Fellows Yates	ff1f28f4f0	Update schema	2022-03-25 15:01:25 +01:00