182 commits

Author	SHA1	Message	Date
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +01:00
James Fellows Yates	0a0dffa37c	Try separating MALT	2022-12-04 12:06:33 +01:00
Sofia Stamouli	7e7299203c	Set values to false	2022-12-02 08:55:23 +01:00
sofstam	6d140c683a	Merge branch 'dev' into update_motus	2022-12-01 18:49:23 +01:00
James A. Fellows Yates	80c25008d0	Merge pull request #177 from nf-core/sep-krakenuniq-test ... Separate KrakenUniq test run	2022-12-01 17:34:30 +01:00
James A. Fellows Yates	a34b240dfc	Merge pull request #174 from nf-core/malt-update ... Update MALT	2022-12-01 13:58:30 +01:00
James Fellows Yates	f960c14caf	Fix typos	2022-12-01 13:46:57 +01:00
sofstam	38a818fd17	Apply review suggestions	2022-12-01 13:42:21 +01:00
James A. Fellows Yates	ef1d2da179	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-12-01 12:53:34 +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
James Fellows Yates	d7fbe55849	Add KU to the test profiles and add id to KU processes	2022-11-29 14:19:01 +01:00
Sofia Stamouli	7e3ece53bd	Update modules.config	2022-11-29 13:31:00 +01:00
Sofia Stamouli	0088b07220	Fix trailing whitespace	2022-11-29 13:28:04 +01:00
James A. Fellows Yates	770a35d7ac	Update conf/modules.config	2022-11-29 12:49:20 +01:00
Sofia Stamouli	ba727a81ae	Fix left-padding spaces	2022-11-29 12:45:14 +01:00
Sofia Stamouli	71b52b9c94	Apply review suggestions	2022-11-29 11:58:23 +01:00
sofstam	49af33f68e	Include NCBI_id, read counts and mgc arguments in motus	2022-11-29 11:07:29 +01:00
James A. Fellows Yates	f114cc4122	Apply suggestions from code review	2022-11-24 16:55:19 +01:00
James A. Fellows Yates	17b1e3df1c	Update test.config	2022-11-24 16:53:39 +01:00
James Fellows Yates	a20b3e3c58	Try to reduce MALT memory	2022-11-24 15:51:12 +01:00
James Fellows Yates	9feb6c2db6	Update MALT	2022-11-24 14:44:04 +01:00
Sofia Stamouli	d2195e9eda	Merge branch 'dev' into short_reads_samtools	2022-11-04 11:47:36 +01:00
Sofia Stamouli	b5e6639f9d	Apply review suggestions	2022-11-03 14:12:05 +01:00
James A. Fellows Yates	bc671c547d	Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict ... Fix porechop conflict	2022-11-03 14:08:13 +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 Fellows Yates	d487a1ff2f	Addd FASTP adadapter list	2022-11-02 12:39:34 +01:00
Sofia Stamouli	e4307ad8ab	Change modules.config to include porechop_porechop	2022-11-01 20:50:42 +01:00
Mahwash Jamy	febcbfc057	add missing parameters to nextflow.config	2022-10-31 16:07:53 +00:00
Mahwash Jamy	3147a80a56	Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module	2022-10-31 15:36:57 +00:00
Sofia Stamouli	0e0c55d3b0	Update modules.config	2022-10-31 12:35:51 +01:00
Sofia Stamouli	a4b5fa9f57	Fix trailing space	2022-10-31 12:17:49 +01:00
Sofia Stamouli	1d1047374b	Fix EditorConfig format	2022-10-31 12:09:25 +01:00
Sofia Stamouli	c4a7d094c8	Fix EditorConfig check	2022-10-28 14:33:44 +02:00
Sofia Stamouli	5b99d9024a	Add samtools stats for short-reads	2022-10-28 14:24:33 +02:00
Sofia Stamouli	f87131c7b1	Save samtools stats output	2022-10-28 14:10:24 +02:00
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
Mahwash Jamy	f4717be9ab	add krakenuniq to modules.config	2022-10-25 09:50:44 +00:00
Moritz E. Beber	60e369aa5c	fix: set default run bracken to false	2022-10-21 10:47:51 +02:00
Moritz E. Beber	c7c7a7f678	refactor: change Bracken prefix to be more specific	2022-10-19 16:20:09 +02:00
Sofia Stamouli	7881ba9aef	Fix the amount of left-padding spaces	2022-10-18 17:50:49 +02:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
Moritz E. Beber	767663d975	chore: add Bracken to test configs	2022-10-14 12:18:55 +02:00
Moritz E. Beber	ca38d002de	feat: integrate Bracken into the profiling pipeline	2022-10-14 12:18:07 +02:00
James A. Fellows Yates	3ca9058b9c	Merge pull request #133 from rafalstepien/add-pep-support ... Add working version of PEP-nf-core integration	2022-09-30 10:21:15 +02:00
James Fellows Yates	43a8aa4405	Remove detect_reads.py and replace remaining checks with nextflow code instead	2022-09-27 15:32:51 +02:00
Rafal Stepien	9349346864	Remove --pep parameter and leave just --input	2022-09-16 10:14:01 -04:00