136 commits

Author	SHA1	Message	Date
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
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	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
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	abbbf9c7ab	Update to use tar module compatible for our test databases	2022-09-14 11:16:28 +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	f087136ec9	use proper working FASTP module	2022-09-09 11:12:47 +02:00
James Fellows Yates	60224e9149	Patch fastp until I have an OK on the module update	2022-09-08 14:25:23 +02:00
James Fellows Yates	fc26948950	Fix MultiQC	2022-09-08 12:49:38 +02:00
James Fellows Yates	d11257b330	Module update	2022-09-08 08:08:36 +02:00
James A. Fellows Yates	28d8d3f8fb	Merge branch 'dev' into nf-core-template-merge-2.5	2022-08-31 09:16:34 +02:00
nf-core-bot	6dfca81761	Template update for nf-core/tools version 2.5	2022-08-30 13:43:03 +00:00
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	64f01fcfe0	Merge branch 'dev' into porechop-log	2022-07-20 14:05:23 +02:00
James Fellows Yates	33a5402b25	Add emitting porechop logs to multiqc and fix collection of others	2022-07-19 13:50:39 +02:00
sofstam	3f5fa8cc7a	Merge branch 'dev' into update_filtlong	2022-07-19 13:50:28 +02:00
mjamy	035b4b7a17	Update the dev branch with the DIAMOND module update	2022-07-15 16:28:07 +02:00
James A. Fellows Yates	c215ed5607	Merge branch 'dev' into motus/merge	2022-07-15 10:52:42 +02:00
sofstam	6b00360ff5	Merge branch 'dev' into update_filtlong	2022-07-15 10:05:43 +02:00
James Fellows Yates	eaa69b65d8	Update mOTUs profile module and mix log for multiqc	2022-07-13 12:38:30 +02:00
sofstam	4a316df209	Update the dev branch with the filtlong update	2022-07-12 17:15:36 +02:00
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	447b8f0905	Get fixed Krona module and add Krona taxonomy to test profile	2022-07-01 17:21:19 +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
James A. Fellows Yates	913080a5b1	Merge pull request #96 from MillironX/feature/kaiju2krona ... Add Krona output for Kaiju profiles	2022-06-29 09:27:25 +02:00
James A. Fellows Yates	5e554a3a0b	Merge pull request #91 from MillironX/feature/kreport2krona ... Add Krona output for Kraken classification	2022-06-27 16:55:55 +02:00
Thomas A. Christensen II	5b80c7cab9	Install KAIJU_KAIJU2KRONA	2022-06-27 08:58:28 -05:00
James Fellows Yates	4ff2145e44	Roll back MALT version	2022-06-20 08:23:14 +02:00
Thomas A. Christensen II	5da8d5b741	Install KRONA_KTIMPORTTEXT	2022-06-14 10:34:34 -05:00
Thomas A. Christensen II	a84f693479	Install KRAKENTOOLS_KREPORT2KRONA module	2022-06-14 08:13:36 -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 Fellows Yates	16ec5bf74a	Update parameter names	2022-05-31 20:11:19 +02:00
James Fellows Yates	310ac6b450	Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong	2022-05-31 13:05:52 +02:00
JIANHONG OU	68d0cc00fa	add motus profile.	2022-05-23 08:05:06 -04:00
James Fellows Yates	87a1d80519	Add working output for Kraken2/Centrifuge/DIAMOND	2022-05-07 05:22:35 +02:00
ljmesi	59c7f5a5b1	Update samtools/bam2fq	2022-05-05 08:38:41 +02:00
ljmesi	f4abbe280a	Fix back to nf-core modules version	2022-05-03 12:56:49 +02:00
ljmesi	58d4dec70b	Update samtools view	2022-05-03 11:09:54 +02:00
ljmesi	afdebaf09a	Remove own modification to a module	2022-05-03 10:15:11 +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	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
sofstam	c00ca1c2b8	Add centrifuge kreport in taxprofiler	2022-04-22 15:24:10 +02:00
Sofia Stamouli	236141f065	Resolve conflicts with dev	2022-04-20 10:17:10 +02:00
James A. Fellows Yates	6fecb3eeb7	Merge pull request #54 from nf-core/dev ... Get upstream changes	2022-04-16 06:17:33 +02:00
sofstam	68ce5843a4	Add kaiju in taxprofiler	2022-04-13 18:51:56 +02:00
James Fellows Yates	de57340526	Start work	2022-04-13 11:49:35 +02:00
James A. Fellows Yates	025083061e	Merge branch 'dev' into hostremoval	2022-04-11 13:36:03 +02:00
Sofia Stamouli	fd5ebea9a6	Remove old centrifuge module	2022-04-08 10:57:58 +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
James A. Fellows Yates	23fb319779	Merge branch 'dev' into complexity-filter-bbduk	2022-04-05 13:11:15 +02:00
Moritz E. Beber	c54c32c494	chore: update adapterremoval	2022-04-05 10:18:34 +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	482112bb42	Start work on host removal	2022-04-03 07:58:40 +02:00
James Fellows Yates	b055df5ea0	Add bbduk complexity (entropy-based) filtering	2022-04-02 17:02:05 +02:00
Moritz E. Beber	4d2960c06f	chore: add metaphlan3 module	2022-04-02 14:59:44 +02:00
James Fellows Yates	c4c93bd59d	Start working on adding adapterremoval	2022-03-31 15:31:45 +02:00
sofstam	37a70dc3e3	Merge branch 'dev' into classification_centrifuge	2022-03-25 16:18:35 +01:00
James A. Fellows Yates	edce6603ef	Merge branch 'dev' into nf-core-template-merge-2.3.2	2022-03-24 14:10:58 +01:00
sofstam	3ff54e620e	Add centrifuge classification	2022-03-24 13:02:25 +01:00
nf-core-bot	6b939e6728	Template update for nf-core/tools version 2.3.1	2022-03-23 13:57:56 +00:00
James A. Fellows Yates	3079f16861	Merge branch 'dev' into database-untar	2022-03-21 19:55:36 +01:00
James A. Fellows Yates	631c115e10	Adds PoC of untarring system	2022-03-21 14:58:19 +00:00
James Fellows Yates	c7f022008c	Start getting database prep ready	2022-03-21 15:07:59 +01:00
ljmesi	16be676d72	Add Porechop module	2022-03-18 14:34:10 +01:00
James Fellows Yates	e39c6a8ccb	Fix MALT multiqc report clash	2022-03-03 18:04:03 +01:00
James Fellows Yates	2c183ed2ed	Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue)	2022-03-03 17:42:02 +01:00
James Fellows Yates	cf55cc592c	Get skeleton read processing to input for profiling	2022-02-18 16:51:01 +01:00
James Fellows Yates	12e7b428f2	initial template build from nf-core/tools, version 2.2	2022-02-18 07:55:14 +01:00