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Author	SHA1	Message	Date
sofstam	49af33f68e	Include NCBI_id, read counts and mgc arguments in motus	2022-11-29 11:07:29 +01:00
Sofia Stamouli	f8b769a8f0	Merge pull request #172 from genomic-medicine-sweden/update_samtools_stats ... Include the mapped reads in samtools stats	2022-11-23 10:21:47 +01:00
sofstam	481f90589c	Apply review suggestions	2022-11-23 09:08:22 +01:00
Moritz E. Beber	b6f5930b49	Merge pull request #171 from nf-core/chore-fail-slow ... chore: let all tests run to completion	2022-11-22 19:22:14 +01:00
sofstam	30af26a8b3	Include the mapped reads in samtools stats	2022-11-22 16:50:50 +01:00
Moritz E. Beber	6b538d658a	chore: let all tests run to completion	2022-11-22 10:13:10 +01:00
James A. Fellows Yates	10c72f1265	Merge pull request #169 from nf-core/diagram-update ... Update tubemap to include samtools stats	2022-11-06 10:15:56 +01:00
James Fellows Yates	f414f5dc9c	Add falco to tube map	2022-11-04 18:20:44 +01:00
James Fellows Yates	4275640d9b	update tubemap to include samtools stats	2022-11-04 15:24:15 +01:00
James A. Fellows Yates	67e264b7a9	Merge pull request #162 from genomic-medicine-sweden/short_reads_samtools ... Add samtools stats for short-reads	2022-11-04 14:39:29 +01:00
Sofia Stamouli	696edfb866	Apply prettier	2022-11-04 12:05:23 +01:00
Sofia Stamouli	d2195e9eda	Merge branch 'dev' into short_reads_samtools	2022-11-04 11:47:36 +01:00
Sofia Stamouli	79dd3930bb	Add samtools to README	2022-11-03 16:52:01 +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 A. Fellows Yates	62f45c8be7	Update nextflow.config	2022-11-03 10:03:27 +01:00
James A. Fellows Yates	24dc2a2cec	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-11-03 10:03:07 +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
Sofia Stamouli	3faea8aac5	Fix porechop conflict	2022-11-01 17:34:37 +01:00
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	074d3ec204	Merge pull request #161 from genomic-medicine-sweden/samtools_stats ... Add samtools stats for long-reads	2022-10-31 10:59:37 +01:00
Sofia Stamouli	ce611d6efd	Add bowtie2 mapped reads	2022-10-31 10:04:51 +01:00
Sofia Stamouli	f1778acf35	Apply review suggestion	2022-10-31 09:31:13 +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
Sofia Stamouli	1bd6dbfe58	Add samtools stats for long-reads	2022-10-28 11:40:50 +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	10f7f9e5de	Merge branch 'adapterremoval-fix' of https://github.com/nf-core/taxprofiler into adapterremoval-fix	2022-10-27 12:23:52 +00:00
James A. Fellows Yates	08d61065e5	Add adapterlist to AR2 subworkflow	2022-10-27 12:23:27 +00:00
nf-core-bot	a402ee3be2	[automated] Fix linting with Prettier	2022-10-27 12:20:08 +00:00
James A. Fellows Yates	733d3dc8c5	Apply suggestions from code review	2022-10-27 14:19:28 +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	e658fab430	fix: remove def ... No idea why, must have something to do with scope.	2022-10-27 11:50:47 +02:00
Moritz E. Beber	dd1a4ff158	refactor: only combine same database name ... [skip ci]	2022-10-27 11:19:14 +02:00
Moritz E. Beber	0de1ac5356	docs: add Bracken reference	2022-10-27 10:14:57 +02:00
Sofia Stamouli	63c260bfbc	Merge pull request #148 from genomic-medicine-sweden/add_falco ... Add Falco as an alternative to FastQC	2022-10-25 12:40:26 +02:00
Sofia Stamouli	de6816ec49	Update nextflow_schema.json ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-10-25 11:19:16 +02:00
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
nf-core-bot	00038db634	[automated] Fix linting with Prettier	2022-10-25 08:51:58 +00:00
Sofia Stamouli	d3d4297ca9	Apply review suggestions	2022-10-24 16:28:07 +02:00
Moritz E. Beber	ca7dc308cb	Apply suggestions from code review ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-10-21 16:36:35 +02:00
Moritz E. Beber	60e369aa5c	fix: set default run bracken to false	2022-10-21 10:47:51 +02:00
Moritz E. Beber	7bd6112133	docs: describe Bracken database usage	2022-10-21 10:18:11 +02:00
Moritz E. Beber	385507ec6f	refactor: use tool name 'bracken' only	2022-10-21 10:03:36 +02:00