281 commits

Author	SHA1	Message	Date
James Fellows Yates	8939ce3e20	Start adding bracken/combinebrackenreports (need smodule update)	2022-12-11 16:52:34 +01:00
Moritz E. Beber	24e5bc5410	refactor: use shorter and more explicit syntax	2022-12-04 21:54:10 +01:00
Moritz E. Beber	4529e7e545	refactor: change parameter exclude unmerged to include	2022-12-04 21:36:12 +01:00
James Fellows Yates	0dccfddc24	Switch order back	2022-12-03 21:38:25 +01:00
James A. Fellows Yates	cf8ad96771	Update subworkflows/local/profiling.nf	2022-12-02 15:09:08 +01:00
James Fellows Yates	ab42f6b662	wteak message	2022-12-02 12:49:00 +01:00
James Fellows Yates	a3cd188b1f	Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test	2022-12-02 12:48:18 +01:00
James Fellows Yates	de74e4f727	Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md	2022-12-02 12:47:14 +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 A. Fellows Yates	4f6eb6fd75	Merge pull request #153 from mjamy/add-krakenuniq-module ... Add krakenuniq module	2022-12-01 09:03:29 +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
Moritz E. Beber	ddcf38de22	refactor: make mappings explicit	2022-11-29 10:14:20 +01:00
James Fellows Yates	9feb6c2db6	Update MALT	2022-11-24 14:44:04 +01:00
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
James Fellows Yates	06659af777	Remove flatten	2022-11-22 13:36:40 +01:00
James Fellows Yates	ebfc84e235	Does the grouping work if we have meta?	2022-11-22 13:26:54 +01:00
James Fellows Yates	21759807f7	Does flatten work?	2022-11-22 12:48:54 +01:00
James Fellows Yates	3102e40052	dump teh db	2022-11-22 12:46:26 +01:00
James Fellows Yates	557f2a4d96	Extra dump	2022-11-22 12:26:46 +01:00
James Fellows Yates	5caebcc6ab	Append to correct db	2022-11-22 12:21:59 +01:00
James Fellows Yates	52fc00802b	Correct meta name for db meta	2022-11-22 12:19:56 +01:00
James Fellows Yates	b8937748d3	Fix meta.id isssue	2022-11-22 12:18:52 +01:00
James Fellows Yates	db334c5185	Fix missing info	2022-11-22 12:17:08 +01:00
James Fellows Yates	0f298dca43	group krakenuniq reads by pairs or single end	2022-11-22 12:13:08 +01:00
Sofia Stamouli	d2195e9eda	Merge branch 'dev' into short_reads_samtools	2022-11-04 11:47:36 +01:00
James Fellows Yates	461482d22a	Try again wit hthe corret param	2022-11-03 15:02:22 +01:00
James Fellows Yates	93f38b14a8	Save report	2022-11-03 15:01:00 +01:00
James Fellows Yates	21a76c2449	Fix cardinality issue	2022-11-03 14:56:26 +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
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	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
Mahwash Jamy	86ca71cfd4	include krakenuniq in profiling subworkflow	2022-10-25 09:45:05 +00:00
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
James Fellows Yates	d19a473c59	Merge branch 'filtlong-in-tests' into json-schema	2022-08-30 14:33:19 +02:00
James Fellows Yates	3f8f32cba8	Make longread quality ftilering opt out	2022-08-30 14:08:05 +02:00
James Fellows Yates	2cc07183a0	Standardise QC parameter system and turn on both porechop/filtlong in tests	2022-08-30 13:58:58 +02:00
James Fellows Yates	d4af88e3ff	Make kaiju parameter clearer for documentation purpses and update documentation	2022-08-25 15:50:28 +02:00
James A. Fellows Yates	de70b0a01d	Merge pull request #109 from nf-core/centrifuge_mqc ... Trying to get Centrifuge output into MQC	2022-07-29 13:36:25 +02:00
James A. Fellows Yates	f48b22d615	Apply suggestions from code review	2022-07-29 09:52:49 +02:00
James Fellows Yates	873a13e028	Merge remote-tracking branch 'origin/dev' into porechop-log	2022-07-29 09:51:34 +02:00
Mahwash Jamy	49487593e2	Merge branch 'nf-core:dev' into diamond-update	2022-07-28 15:48:59 +02:00
sofstam	cecbb41f88	Update centrifuge/kreport	2022-07-27 14:42:35 +02:00
James A. Fellows Yates	9d2be68fb8	Merge branch 'dev' into centrifuge_mqc	2022-07-26 18:01:30 +00:00
James A. Fellows Yates	1ef0975736	Merge branch 'dev' into porechop-log	2022-07-26 18:00:28 +00:00
James A. Fellows Yates	3054dea7c2	Get multiqc input working	2022-07-26 08:41:06 +00:00
James A. Fellows Yates	e76b299705	Start working getting kraken and centrifuge working in MQC	2022-07-26 08:18:54 +00:00
James Fellows Yates	139cf0d6aa	Fix	2022-07-26 10:12:33 +02:00
James A. Fellows Yates	64f01fcfe0	Merge branch 'dev' into porechop-log	2022-07-20 14:05:23 +02:00
James Fellows Yates	255afee4c7	Re-add the collects	2022-07-19 17:10:10 +02:00
Mahwash Jamy	811ded38af	Update subworkflows/local/profiling.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-07-19 16:44:48 +02:00
Sofia Stamouli	237e9aa623	Update longread_preprocessing.nf	2022-07-19 16:44:08 +02:00
James A. Fellows Yates	8d7ddb5847	Apply suggestions from code review	2022-07-19 16:30:13 +02:00
mjamy	c4c82212e1	incorporate diamond log file into multiqc channel	2022-07-19 14:12:16 +02:00
sofstam	171258d545	Fix typos	2022-07-19 14:07:13 +02:00
sofstam	25bc01f9c4	Fix typos	2022-07-19 14:04:49 +02:00