160 commits

Author	SHA1	Message	Date
Moritz E. Beber	fdb8a7f740	Merge branch 'devel' into nf-core-template-merge-2.6	2022-10-05 12:21:54 +02:00
nf-core-bot	51bacb00e6	Template update for nf-core/tools version 2.6	2022-10-05 03:30:53 +00:00
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
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	63b3cc678f	Merge branch 'motus-merge-meta' of github.com:nf-core/taxprofiler into motus-merge-meta	2022-09-16 10:25:28 +02:00
James Fellows Yates	c5cc21d29e	Update motus merge module to remove unused channel	2022-09-16 10:25:24 +02:00
James A. Fellows Yates	2c83b367a7	Apply suggestions from code review	2022-09-16 09:28:42 +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 A. Fellows Yates	5414ae2e55	Apply suggestions from code review	2022-09-14 11:20:40 +02:00
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 A. Fellows Yates	b28052f1ec	Remove patch from modules.json	2022-09-09 11:15:25 +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
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	9bc45a3f24	Update centrifuge/kreport	2022-07-27 14:44:26 +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 Fellows Yates	d83c747533	Fix modules JSON	2022-07-15 12:38:20 +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	1fbe241d27	Update filtlong module	2022-07-12 17:43:52 +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	2838c136bd	Prettier	2022-06-02 12:51:39 +02:00
James Fellows Yates	fa70a413cb	Use finally working filtlong module	2022-05-31 21:12:09 +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	f14141574e	fix the end line issue for modules.json	2022-05-25 08:03:23 -04:00
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	5b7b214156	Fix formatting with prettier	2022-05-05 08:40:53 +02:00
ljmesi	59c7f5a5b1	Update samtools/bam2fq	2022-05-05 08:38:41 +02:00
ljmesi	c833d4fd9a	Fix issues found with prettier	2022-05-03 11:42:05 +02:00
ljmesi	58d4dec70b	Update samtools view	2022-05-03 11:09:54 +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
Sofia Stamouli	f4480feb9b	Prettier	2022-04-25 17:45:26 +02:00
sofstam	d082d67bcb	Add kaiju2table to taxprofiler	2022-04-25 17:36:29 +02:00
Sofia Stamouli	ba2479b95b	Prettier	2022-04-25 09:26:49 +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 Fellows Yates	d0256ec937	Prettier	2022-04-16 07:45:24 +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	6736a2a980	Update README.md, nextflow_schema.json	2022-04-13 19:00:52 +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	63bc597daf	Prettier	2022-04-08 11:01:45 +02:00
Sofia Stamouli	fd5ebea9a6	Remove old centrifuge module	2022-04-08 10:57:58 +02:00
Sofia Stamouli	3d45ac57ae	Prettier	2022-04-07 16:42:22 +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	59b2088aa1	style: apply prettier	2022-04-05 11:16:43 +02:00
Moritz E. Beber	c54c32c494	chore: update adapterremoval	2022-04-05 10:18:34 +02:00
James Fellows Yates	bb6dd738bd	Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk	2022-04-04 21:21:34 +02:00
James Fellows Yates	613f6a5565	Prettier	2022-04-04 21:21:29 +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 Fellows Yates	a76576c16b	Prettier	2022-04-03 17:24:50 +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	b04cfec2c2	Prettier linting	2022-04-01 11:13:36 +02:00
James Fellows Yates	c4c93bd59d	Start working on adding adapterremoval	2022-03-31 15:31:45 +02:00
James Fellows Yates	eada201eb2	Prettier	2022-03-28 16:47:37 +02:00
James Fellows Yates	98dc8014a5	Fix kraken2 module	2022-03-28 16:46:45 +02:00
sofstam	16bdc79cc0	Apply prettier	2022-03-25 16:30:26 +01:00
sofstam	37a70dc3e3	Merge branch 'dev' into classification_centrifuge	2022-03-25 16:18:35 +01:00
James Fellows Yates	494c641fb8	Prettier	2022-03-24 15:37:42 +01:00
James Fellows Yates	e3be393f16	Fix broken json	2022-03-24 14:18:15 +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