203 commits

Author	SHA1	Message	Date
sofstam	481f90589c	Apply review suggestions	2022-11-23 09:08:22 +01:00
sofstam	30af26a8b3	Include the mapped reads in samtools stats	2022-11-22 16:50:50 +01:00
Sofia Stamouli	d2195e9eda	Merge branch 'dev' into short_reads_samtools	2022-11-04 11:47:36 +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	3faea8aac5	Fix porechop conflict	2022-11-01 17:34:37 +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	5b99d9024a	Add samtools stats for short-reads	2022-10-28 14:24:33 +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	08d61065e5	Add adapterlist to AR2 subworkflow	2022-10-27 12:23:27 +00:00
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
Sofia Stamouli	8c3e80b6ea	Add helptest to nextflow_schema,add versions to longread_preprocessing	2022-10-25 11:13:26 +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	385507ec6f	refactor: use tool name 'bracken' only	2022-10-21 10:03:36 +02:00
Sofia Stamouli	511cb16a61	Apply review suggestions	2022-10-20 16:55:57 +02:00
Moritz E. Beber	8deb7757d8	fix: remove Bracken from standardise reports	2022-10-19 16:21:57 +02:00
Moritz E. Beber	b73b479860	refactor: handle combined kraken2+bracken tool column	2022-10-19 16:21:36 +02:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
Moritz E. Beber	48b00b7d62	refactor: create standardized Bracken reports	2022-10-17 17:33:24 +02:00
Moritz E. Beber	563b34c9c3	refactor: rename process to kraken2	2022-10-14 14:48:27 +02:00
Moritz E. Beber	95621ebd8a	fix: include local module	2022-10-14 14:47:08 +02:00
Moritz E. Beber	ca38d002de	feat: integrate Bracken into the profiling pipeline	2022-10-14 12:18:07 +02:00
James Fellows Yates	56bae85755	Remove necessity of patch	2022-10-11 12:38:18 +02:00
Moritz E. Beber	180cac0395	fix: adapt to new samtools/view input	2022-10-05 13:49:35 +02:00
Moritz E. Beber	f5af9fd939	fix: adjust import paths to re-organization	2022-10-05 13:40:43 +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	87edc4569c	Move to a function	2022-09-27 15:46:17 +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	1584d6fc51	Update workflows/taxprofiler.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-19 10:43:04 -04:00
James A. Fellows Yates	016efcb807	Merge branch 'dev' into metaphlan3/mergemetaphlantables	2022-09-16 16:02:38 +02:00
James A. Fellows Yates	f43c54317c	Update subworkflows/local/standardisation_profiles.nf ... Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>	2022-09-16 15:20:47 +02:00
James Fellows Yates	c5cc21d29e	Update motus merge module to remove unused channel	2022-09-16 10:25:24 +02:00
James Fellows Yates	4e7857e2ed	Standardise mOTUs table merge	2022-09-16 08:36:34 +02:00
Rafal Stepien	768f9980d8	Add pep_input_base_dir to workflow. Just need to update modules	2022-09-15 12:31:49 -04:00
James A. Fellows Yates	cdb21d17b3	Merge branch 'dev' into metaphlan3/mergemetaphlantables	2022-09-15 13:08:57 +02:00
James Fellows Yates	21ae9d85c3	Ensure merge metaphlan3 tables happens on per database basis	2022-09-15 12:29:54 +02:00
Rafal Stepien	5f3eee9a4a	Add working version of PEP-nf-core integration	2022-09-14 14:28:48 -04:00
James Fellows Yates	05e9d92444	Add centrigue kreports	2022-09-13 16:47:19 +02:00
James Fellows Yates	c8dbf5be47	Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU	2022-09-13 15:47:28 +02:00
James Fellows Yates	a764bc4807	Start works - need updated module though t have meta	2022-09-09 13:57:06 +02:00
James A. Fellows Yates	cc5df924e4	Merge branch 'dev' into module-update	2022-09-08 13:36:21 +02:00
James Fellows Yates	d11257b330	Module update	2022-09-08 08:08:36 +02:00
James Fellows Yates	7c5f9d0c24	Start work on more merging tools	2022-09-06 17:34:45 +02:00
James A. Fellows Yates	8456f934ed	Update subworkflows/local/visualization_krona.nf	2022-09-02 16:15:46 +02:00
James A. Fellows Yates	13e9957e14	Fixes process selector warning	2022-09-02 06:03:05 +00:00