127 commits

Author	SHA1	Message	Date
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
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