69 commits

Author	SHA1	Message	Date
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
James A. Fellows Yates	96fecb2bfc	Merge branch 'dev' into support-aligned-reads	2022-06-03 13:48:54 +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
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