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Author	SHA1	Message	Date
James Fellows Yates	7f1a7fb4e7	Add complexity filtering to test profile	2022-04-02 17:05:54 +02:00
Moritz E. Beber	4eab257d68	style: prettify comment	2022-04-02 17:05:46 +02:00
James Fellows Yates	b055df5ea0	Add bbduk complexity (entropy-based) filtering	2022-04-02 17:02:05 +02:00
Moritz E. Beber	41526e8a64	try to fix locale	2022-04-02 15:44:39 +02:00
Moritz E. Beber	4e22bc9610	fix: force UTF-8 in different locale?	2022-04-02 15:20:36 +02:00
Moritz E. Beber	562fa42696	fix: remove duplicate porechop entry	2022-04-02 15:00:55 +02:00
Moritz E. Beber	70862570e0	fix: use same naming scheme	2022-04-02 15:00:26 +02:00
Moritz E. Beber	817678d870	chore: add metaphlan3 run to test profile	2022-04-02 15:00:26 +02:00
Moritz E. Beber	996b3f4912	fix: correct the input shape to metaphlan3	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
Moritz E. Beber	95ed86516b	chore: add citation	2022-04-02 15:00:26 +02:00
Moritz E. Beber	e579f9f5f3	style: apply prettier	2022-04-02 14:59:44 +02:00
Moritz E. Beber	fb9afa013a	fix: add metaphlan parameter to schema	2022-04-02 14:59:44 +02:00
Moritz E. Beber	a425a322f2	refactor: make metaphlan3 run in workflow	2022-04-02 14:59:44 +02:00
Moritz E. Beber	69db920610	feat: include metaphlan3 in workflow	2022-04-02 14:59:44 +02:00
Moritz E. Beber	4d2960c06f	chore: add metaphlan3 module	2022-04-02 14:59:44 +02:00
James A. Fellows Yates	1dfbcacf68	Merge pull request #34 from nf-core/adapterremoval ... Add AdapterRemoval as alternative trimer/merger	2022-04-02 10:33:45 +02:00
James Fellows Yates	93aaa9eeac	Clean up AdapterRemoval and remove all debugging dumps	2022-04-01 21:36:22 +02:00
James A. Fellows Yates	03e832954f	Update subworkflows/local/shortread_adapterremoval.nf ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-01 20:55:33 +02:00
James A. Fellows Yates	14f2b7bd84	Apply suggestions from code review ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-04-01 15:34:05 +02:00
James Fellows Yates	0d0b377dfb	Add additional test	2022-04-01 11:19:00 +02:00
James Fellows Yates	df4f13319f	More linting	2022-04-01 11:13:57 +02:00
James Fellows Yates	b04cfec2c2	Prettier linting	2022-04-01 11:13:36 +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	c4c93bd59d	Start working on adding adapterremoval	2022-03-31 15:31:45 +02:00
James A. Fellows Yates	323883bd3e	Merge pull request #33 from nf-core/improve-shortread-input ... Improve shortread input preprocessing	2022-03-30 11:48:32 +02:00
James Fellows Yates	76e9624e3f	NOW commit the adapte rtrim flag	2022-03-30 11:31:37 +02:00
James Fellows Yates	98a9688329	Change CPUs back to template, update skiptrim fiag	2022-03-29 15:18:06 +02:00
Sofia Stamouli	c552819c72	Apply prettier again	2022-03-28 22:15:31 +02:00
sofstam	d25f97c506	Prettier format	2022-03-28 22:08:05 +02:00
James Fellows Yates	04fb6f4127	Use new resources for test data	2022-03-28 20:38:16 +02:00
James Fellows Yates	94e5cfef4a	Filter long reads for MALT, bump cpus for FastQC for minigut to pass	2022-03-28 18:20:10 +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
James Fellows Yates	231253227c	Remove run merging for now due to complexity	2022-03-28 16:38:10 +02:00
sofstam	0e0e8128e8	Prettier format	2022-03-28 13:53:16 +02:00
James Fellows Yates	ee53283696	Debugging comment	2022-03-28 09:13:05 +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 A. Fellows Yates	622fafedc8	Prempt centrifuge database untar crash	2022-03-26 20:22:35 +00:00
James Fellows Yates	120382f51d	Fix input channels to kraken2	2022-03-26 06:45:16 +01:00
sofstam	59d3f18a75	Update nextflow_schema.json	2022-03-25 17:18:04 +01:00
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 A. Fellows Yates	000f129dab	Apply suggestions from code review	2022-03-25 15:32:56 +01:00
James Fellows Yates	ede362dbf9	Remove duplicate config and sync longread fastqc	2022-03-25 15:28:30 +01:00
James Fellows Yates	b763bfa2c0	More cleanup	2022-03-25 15:26:57 +01:00
James Fellows Yates	0e6f7e2ca1	Revert "Some more cleanup" ... This reverts commit 7ddcb09a85.	2022-03-25 15:24:10 +01:00
James Fellows Yates	7ddcb09a85	Some more cleanup	2022-03-25 15:22:41 +01:00
James Fellows Yates	b5f5c75504	Fix file header descriptions	2022-03-25 15:21:52 +01:00