139 commits

Author	SHA1	Message	Date
James Fellows Yates	6895e45768	Fix a few conditional bugs and related	2023-03-23 15:46:02 +01:00
James Fellows Yates	3b90064ba4	Start adding conditions in modules.conf - non-cat not working	2023-03-22 15:39:45 +01:00
sofstam	1347f27c11	Update changelog after release	2023-03-13 12:21:37 +01:00
James Fellows Yates	98bc6910d5	Update authors and remove left over comment	2023-03-07 11:47:54 +01:00
James A. Fellows Yates	f0f89eb082	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 14:58:21 +01:00
James A. Fellows Yates	c66c67524c	Update nextflow.config ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 13:33:41 +01:00
James A. Fellows Yates	6c2ce4a1c9	Apply suggestions from code review ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2023-03-03 08:37:31 +01:00
James Fellows Yates	aedf0b34de	Bump version for release	2023-03-02 13:51:28 +01:00
James Fellows Yates	5c549e5ce3	Remove TODOs and references to under development	2023-03-02 13:49:03 +01:00
Sofia Stamouli	69430ef851	Update nextflow.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-02-27 11:02:55 +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
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	25d44c955e	Merge dev into add_taxpasta_merge	2023-02-16 15:16:05 +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
James A. Fellows Yates	1279437aa1	Apply suggestions from code review	2022-12-20 21:48:08 +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	4b68e95770	Revert PEP validation back to python samplesheet check	2022-12-12 08:49:13 +01:00
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	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
sofstam	38a818fd17	Apply review suggestions	2022-12-01 13:42:21 +01:00
sofstam	e5bb627402	Apply review suggestions	2022-12-01 11:12:31 +01:00
James Fellows Yates	bc98f5b80f	Separate KrakenUniq test run	2022-12-01 10:37:14 +01:00
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
sofstam	49af33f68e	Include NCBI_id, read counts and mgc arguments in motus	2022-11-29 11:07:29 +01:00
James Fellows Yates	c5e5696f84	Fix parameter name	2022-11-03 14:58:03 +01:00
James Fellows Yates	21a76c2449	Fix cardinality issue	2022-11-03 14:56:26 +01:00
James A. Fellows Yates	1f31f88635	Merge pull request #158 from nf-core/adapterremoval-fix ... Fix adapterremoval adapter conflict and add optional adapter list file	2022-11-03 11:36:14 +01:00
James A. Fellows Yates	62f45c8be7	Update nextflow.config	2022-11-03 10:03:27 +01:00
Mahwash Jamy	febcbfc057	add missing parameters to nextflow.config	2022-10-31 16:07:53 +00:00
Moritz E. Beber	bf89525bc2	Merge pull request #146 from nf-core/feat-bracken ... add Bracken to the profiling workflow	2022-10-27 17:35:06 +02:00
James A. Fellows Yates	76a662ecc5	Fix adapterremoval adapter conflict and add optional adapter list file	2022-10-27 12:17:19 +00:00
Moritz E. Beber	60e369aa5c	fix: set default run bracken to false	2022-10-21 10:47:51 +02:00
Sofia Stamouli	511cb16a61	Apply review suggestions	2022-10-20 16:55:57 +02:00
Moritz E. Beber	ca38d002de	feat: integrate Bracken into the profiling pipeline	2022-10-14 12:18:07 +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	5b6c18f0a2	Update nextflow.config ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-19 09:49:28 -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	3eb136ec3c	Merge branch 'dev' into json-schema	2022-08-31 12:55:49 +02:00