104 commits

Author	SHA1	Message	Date
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
James Fellows Yates	4e93abc7c0	Add read improved read preprocessing	2022-03-25 14:58:06 +01:00
James Fellows Yates	92a3c8ec8d	Prettier	2022-03-24 15:40:14 +01:00
James Fellows Yates	494c641fb8	Prettier	2022-03-24 15:37:42 +01:00
James Fellows Yates	cc9368ee52	Prettier linting and update schema	2022-03-24 15:35:09 +01:00
James A. Fellows Yates	edce6603ef	Merge branch 'dev' into nf-core-template-merge-2.3.2	2022-03-24 14:10:58 +01:00
nf-core-bot	6b939e6728	Template update for nf-core/tools version 2.3.1	2022-03-23 13:57:56 +00:00
James A. Fellows Yates	ac77676d2b	Merge branch 'dev' into nf-core-template-merge-2.3	2022-03-17 13:11:34 +01:00
nf-core-bot	699d26b149	Template update for nf-core/tools version 2.3	2022-03-15 21:05:37 +00:00
James Fellows Yates	cf55cc592c	Get skeleton read processing to input for profiling	2022-02-18 16:51:01 +01:00
James Fellows Yates	12e7b428f2	initial template build from nf-core/tools, version 2.2	2022-02-18 07:55:14 +01:00