157 commits

Author	SHA1	Message	Date
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	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	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
James A. Fellows Yates	016efcb807	Merge branch 'dev' into metaphlan3/mergemetaphlantables	2022-09-16 16:02:38 +02:00
James Fellows Yates	4e7857e2ed	Standardise mOTUs table merge	2022-09-16 08:36:34 +02:00
James A. Fellows Yates	cdb21d17b3	Merge branch 'dev' into metaphlan3/mergemetaphlantables	2022-09-15 13:08:57 +02:00
James Fellows Yates	19a195ed14	Append profiler to resulting file	2022-09-15 12:30:39 +02:00
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 Fellows Yates	832d981976	Don't have per sample directory as unnecessary if file names are unique with the db in them	2022-09-07 12:22:17 +02:00
James Fellows Yates	7c5f9d0c24	Start work on more merging tools	2022-09-06 17:34:45 +02:00
James A. Fellows Yates	13e9957e14	Fixes process selector warning	2022-09-02 06:03:05 +00:00
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	a97bb69cd2	Prettier	2022-08-23 14:24:57 +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
mjamy	5cdf5e958a	Updated modules.config to add 'log' in diamond config	2022-07-28 16:08:15 +02:00
sofstam	71cf32cc6a	Add error strategy for centrifuge/kreport	2022-07-28 08:54:32 +02:00
James A. Fellows Yates	65ae82efc4	Define separte krakena nd centrigfue modules	2022-07-26 18:37:33 +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	a0ee82bf43	Add motus/merge and biom support	2022-07-12 11:39:26 +02:00
James A. Fellows Yates	8082c7d108	Merge pull request #97 from nf-core/malt-to-krona ... Add Krona support for MALT	2022-07-05 15:17:52 +02:00
James A. Fellows Yates	26e31c782d	Merge branch 'dev' into motus	2022-07-04 13:14:42 +02:00
James Fellows Yates	02c06b9f7b	Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file	2022-06-30 18:33:11 +02:00
Thomas A. Christensen II	069370db86	Add unclassified and verbose flags to kaiju2krona	2022-06-28 09:00:42 -05:00
Thomas A. Christensen II	0e8edd5b2f	Add output configuration for Kraken Krona chart	2022-06-27 08:25:47 -05:00
JIANHONG OU	c8a59adbce	remove the database auto-download for mOTUs.	2022-06-03 14:13:58 -04:00
James A. Fellows Yates	96fecb2bfc	Merge branch 'dev' into support-aligned-reads	2022-06-03 13:48:54 +02:00
James A. Fellows Yates	53c4399052	Merge branch 'dev' into motus	2022-06-02 21:38:35 +02:00
James A. Fellows Yates	c9581b1796	Merge branch 'dev' into support-aligned-reads	2022-06-02 12:45:29 +02:00
James Fellows Yates	d3d28da1b1	Update after review	2022-06-02 11:53:53 +02:00
James Fellows Yates	16ec5bf74a	Update parameter names	2022-05-31 20:11:19 +02:00
JIANHONG OU	f0eb88cbe2	add mOTUs to modules.config	2022-05-31 08:57:00 -04:00
James Fellows Yates	310ac6b450	Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong	2022-05-31 13:05:52 +02:00
James A. Fellows Yates	d67543503b	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-05-07 13:15:21 +02:00
James Fellows Yates	0f651873dd	Linting	2022-05-07 06:12:24 +02:00
James Fellows Yates	47a5ae0cff	Add FASTP complexity option	2022-05-07 06:09:05 +02:00
James Fellows Yates	87a1d80519	Add working output for Kraken2/Centrifuge/DIAMOND	2022-05-07 05:22:35 +02:00
ljmesi	d94534e8ac	Simplify params which control host removal publish	2022-05-05 09:07:33 +02:00
ljmesi	a821f748ee	Add modules	2022-05-03 09:28:46 +02:00
James Fellows Yates	031cb45934	Add initial longread QC filtering - requires filtlong module update	2022-05-01 07:18:14 +02:00
James Fellows Yates	a4a9b161d8	Lintin	2022-04-29 22:02:44 +02:00
James Fellows Yates	8126d16dee	Add draft version of DIAMOND	2022-04-29 21:59:42 +02:00
sofstam	d082d67bcb	Add kaiju2table to taxprofiler	2022-04-25 17:36:29 +02:00
Sofia Stamouli	e7e24c2d95	Prettier and suggestions from review	2022-04-25 09:21:29 +02:00
sofstam	c00ca1c2b8	Add centrifuge kreport in taxprofiler	2022-04-22 15:24:10 +02:00
James A. Fellows Yates	cd3c8f6a89	Merge branch 'dev' into hostremoval-publish-fix	2022-04-21 11:43:06 +02:00
Sofia Stamouli	236141f065	Resolve conflicts with dev	2022-04-20 10:17:10 +02:00
James A. Fellows Yates	d16cd75652	Merge branch 'dev' into hostremoval-publish-fix	2022-04-20 09:53:51 +02:00
sofstam	1b7ff2265d	Update usage.md, reformat test.config and modules.config	2022-04-19 13:04:58 +02:00
James Fellows Yates	9880baa0b8	Get build directory working	2022-04-18 06:37:23 +02:00
James Fellows Yates	2cfcdf2dd2	Add finer controler over for hostremoval saving	2022-04-17 22:27:04 +02:00
James Fellows Yates	cc73cdd51d	Add generation of taxon-table like output for MALT	2022-04-16 07:42:30 +02:00
sofstam	68ce5843a4	Add kaiju in taxprofiler	2022-04-13 18:51:56 +02:00
James A. Fellows Yates	70f94603b0	Merge branch 'dev' into hostremoval	2022-04-13 13:59:51 +02:00
James Fellows Yates	dfeaa0d1fe	Rename subworkflow parameters for consistency	2022-04-13 12:00:28 +02:00
James A. Fellows Yates	967b1f7d6e	Merge branch 'dev' into run-merging	2022-04-12 09:28:10 +02:00
James Fellows Yates	a5f4fc42d5	Fix run merging for unmerged PE data	2022-04-12 09:25:27 +02:00
James A. Fellows Yates	025083061e	Merge branch 'dev' into hostremoval	2022-04-11 13:36:03 +02:00
James Fellows Yates	082093f3de	Prettier	2022-04-10 06:44:10 +02:00
James Fellows Yates	ecf0eea4f9	Move profiling to subworkflow and standardise outputs	2022-04-10 06:43:30 +02:00
James Fellows Yates	ca011ccc5b	Fix cat_fastq naming logic?	2022-04-08 13:28:37 +02:00
James Fellows Yates	d130a72d74	Get this working	2022-04-08 13:09:23 +02:00
sofstam	606e5da7d5	Check if PR works with centrifuge/centrifuge module	2022-04-07 16:13:17 +02:00
James A. Fellows Yates	b554aa3e4d	Merge branch 'dev' into hostremoval	2022-04-07 14:00:10 +02:00
Moritz E. Beber	7ab3aa546b	refactor: use flags to publish reads	2022-04-06 10:27:11 +02:00
Moritz E. Beber	018b9a8ea6	refactor: do not generally publish output	2022-04-06 10:21:43 +02:00
Moritz E. Beber	8827b143a2	fix: disable publishing correctly	2022-04-05 20:56:19 +02:00
Moritz E. Beber	af12435fa5	fix: use parameter for publish mode everywhere	2022-04-05 20:56:19 +02:00
Moritz E. Beber	c40a9a0011	refactor: avoid publishing unpacked databases	2022-04-05 20:54:32 +02:00
James A. Fellows Yates	3d662d2e06	Merge branch 'dev' into complexity-filter-bbduk	2022-04-04 21:19:36 +02:00
James Fellows Yates	a384162810	Add prinseq as alternative complexity filtering	2022-04-04 21:16:51 +02:00
sofstam	d897c922b2	Add centrifuge classificatioN	2022-04-04 13:51:51 +02:00
James A. Fellows Yates	b2e29ea23a	Merge branch 'dev' into hostremoval	2022-04-03 17:24:07 +02:00
James Fellows Yates	066ceb2bca	Remove flagstat as bowtie2 reports this itself	2022-04-03 17:23:14 +02:00
James Fellows Yates	b055df5ea0	Add bbduk complexity (entropy-based) filtering	2022-04-02 17:02:05 +02:00
Moritz E. Beber	70862570e0	fix: use same naming scheme	2022-04-02 15:00:26 +02:00
Moritz E. Beber	b0b5936fe8	chore: configure output for metaphlan3	2022-04-02 15:00:26 +02:00
James Fellows Yates	dcda815bfb	Add final adapterremoval options to match fastp functionality	2022-04-01 09:50:08 +02:00
James Fellows Yates	76e9624e3f	NOW commit the adapte rtrim flag	2022-03-30 11:31:37 +02:00
James Fellows Yates	231253227c	Remove run merging for now due to complexity	2022-03-28 16:38:10 +02:00
James Fellows Yates	8dc9e583ad	Debugging run merging	2022-03-27 09:30:23 +02:00
James A. Fellows Yates	e6e8ed7cc9	Add some debugging notes	2022-03-26 20:54:50 +00:00
James Fellows Yates	ede362dbf9	Remove duplicate config and sync longread fastqc	2022-03-25 15:28:30 +01:00
James Fellows Yates	ff1f28f4f0	Update schema	2022-03-25 15:01:25 +01:00
James Fellows Yates	4e93abc7c0	Add read improved read preprocessing	2022-03-25 14:58:06 +01:00
sofstam	3ff54e620e	Add centrifuge classification	2022-03-24 13:02:25 +01:00
James Fellows Yates	358b89a4c6	Linting	2022-03-21 20:30:29 +01:00
James Fellows Yates	81bfb629ca	Add working basic test to begin	2022-03-21 20:28:09 +01:00
James A. Fellows Yates	3079f16861	Merge branch 'dev' into database-untar	2022-03-21 19:55:36 +01:00
James Fellows Yates	8012998542	Make parameter naming more consistent for clipmerge	2022-03-21 19:52:50 +01:00