178 commits

Author	SHA1	Message	Date
James A. Fellows Yates	0245c4880b	Merge branch 'dev' into final-reads-saving	2023-04-20 14:18:10 +02:00
James Fellows Yates	ce97a1124e	Add final documentation	2023-04-15 12:48:52 +02:00
sofstam	102d53bd75	Subsitute samtools/bam2fq with samtools/fastq	2023-03-23 15:30:07 +01:00
James Fellows Yates	b0939c3ae9	Standardised taxon table and mOTU database docs improvement	2023-03-17 21:03:54 +01:00
James A. Fellows Yates	eaef6ac9bc	Apply suggestions from code review	2023-03-13 10:57:36 +01:00
James Fellows Yates	e49668005f	Update docs based on feedback and add missing results directories	2023-03-12 08:35:45 +01:00
Sofia Stamouli	df5303270d	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 14:18:30 +01:00
Sofia Stamouli	fff7453d0c	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 14:18:22 +01:00
Sofia Stamouli	9621d34c4a	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 14:18:11 +01:00
Sofia Stamouli	54af021965	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 14:18:01 +01:00
sofstam	99fe8adb1b	Add helptext	2023-02-27 13:49:02 +01:00
Sofia Stamouli	e3e465df1f	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 11:00:59 +01:00
sofstam	489650feb8	Linting	2023-02-27 10:24:14 +01:00
sofstam	2f0c68a833	Last review suggestions	2023-02-27 10:15:42 +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 Fellows Yates	cd4614f387	Fix typo in schema docs [skip ci]	2023-02-23 14:00:00 +01:00
sofstam	04bc978ef6	Remove taxonomy parameter from taxpasta	2023-02-20 11:56:06 +01:00
sofstam	f0aa89cb87	Rename taxpasta parameters and remove samplesheet parameter	2023-02-17 14:47:29 +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	dad64a688d	Add documentation for taxpasta module	2023-02-16 16:33:36 +01:00
sofstam	de6a4214ef	Add taxpasta_merge to taxprofiler	2023-02-16 14:29:52 +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	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
James A. Fellows Yates	1279437aa1	Apply suggestions from code review	2022-12-20 21:48:08 +01:00
Sofia Stamouli	1706555eff	Prettier	2022-12-20 20:10:05 +01:00
Sofia Stamouli	24a8da2086	Fix linting	2022-12-20 19:59:55 +01:00
Sofia Stamouli	d691b89727	Merge branch 'dev' into nf-core-template-merge-2.7.2	2022-12-20 15:14:41 +01:00
nf-core-bot	ab591e01ff	Template update for nf-core/tools version 2.7.2	2022-12-19 12:10:58 +00:00
James Fellows Yates	1ccd0a0767	Merge branch 'dev' into nf-core-template-merge-2.7.1	2022-12-09 10:16:17 +01:00
nf-core-bot	36f3b5723b	Template update for nf-core/tools version 2.7.1	2022-12-08 13:18:23 +00:00
James Fellows Yates	3dba6405c5	Sets correct default for --shortread_qc_mergepairs	2022-12-06 11:47:16 +01:00
Moritz E. Beber	b2088bcbb3	docs: improve description of shortread_qc_includeunmerged	2022-12-04 21:53:38 +01:00
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +01:00
sofstam	6d140c683a	Merge branch 'dev' into update_motus	2022-12-01 18:49:23 +01:00
nf-core-bot	410196c37b	[automated] Fix linting with Prettier	2022-12-01 14:33:34 +00:00
sofstam	4800a5f03e	Update schema	2022-12-01 14:23:40 +01:00
sofstam	38a818fd17	Apply review suggestions	2022-12-01 13:42:21 +01:00
sofstam	1965ade961	Update schema	2022-12-01 11:32:51 +01:00
sofstam	e5bb627402	Apply review suggestions	2022-12-01 11:12:31 +01:00
nf-core-bot	8067012c01	[automated] Fix linting with Prettier	2022-12-01 09:15:35 +00:00
James A. Fellows Yates	4f6eb6fd75	Merge pull request #153 from mjamy/add-krakenuniq-module ... Add krakenuniq module	2022-12-01 09:03:29 +01:00
sofstam	933b820c19	Apply review suggestions	2022-11-29 16:57:07 +01:00
Sofia Stamouli	e85c75dcba	Merge branch 'dev' into update_motus	2022-11-29 15:12:31 +01:00
sofstam	12dd836e9c	Fix conflict	2022-11-29 15:00:27 +01:00
sofstam	f389029848	Fix merge conflic	2022-11-29 14:38:39 +01:00
Sofia Stamouli	71b52b9c94	Apply review suggestions	2022-11-29 11:58:23 +01:00