431 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
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
James Fellows Yates	dfcf8f7b1a	Prettier	2022-03-25 15:10:52 +01:00
James Fellows Yates	ff1f28f4f0	Update schema	2022-03-25 15:01:25 +01:00
James Fellows Yates	4e93abc7c0	Add read improved read preprocessing	2022-03-25 14:58:06 +01:00
James A. Fellows Yates	fafb7e0f6f	Update README.md	2022-03-24 16:59:12 +01:00
James A. Fellows Yates	f3c21203c8	Merge pull request #32 from nf-core/nf-core-template-merge-2.3.2 ... Important! Template update for nf-core/tools v2.3.2	2022-03-24 15:50:38 +01:00
James Fellows Yates	92a3c8ec8d	Prettier	2022-03-24 15:40:14 +01:00
James Fellows Yates	494c641fb8	Prettier	2022-03-24 15:37:42 +01:00
James Fellows Yates	cc9368ee52	Prettier linting and update schema	2022-03-24 15:35:09 +01:00
James Fellows Yates	203cd2e7d3	Prettier	2022-03-24 14:31:53 +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	feeb8ba8dd	Template update for nf-core/tools version 2.3.2	2022-03-24 11:48:43 +00:00
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	038a8d106a	Fix test with correct URL	2022-03-23 11:25:47 +01:00
James Fellows Yates	48b6ef508d	Update path to samplesheet	2022-03-23 10:06:01 +01:00
James Fellows Yates	358b89a4c6	Linting	2022-03-21 20:30:29 +01:00
James Fellows Yates	81bfb629ca	Add working basic test to begin	2022-03-21 20:28:09 +01:00
James A. Fellows Yates	cd9e3c604c	Merge pull request #30 from nf-core/database-untar ... Adds ability to conditionally untar databases TAR files that contain DB directories	2022-03-21 19:56:22 +01:00
James A. Fellows Yates	3079f16861	Merge branch 'dev' into database-untar	2022-03-21 19:55:36 +01:00
James Fellows Yates	07eed435c6	Replace set with explicity assignment	2022-03-21 19:54:51 +01:00
James Fellows Yates	8012998542	Make parameter naming more consistent for clipmerge	2022-03-21 19:52:50 +01:00
James A. Fellows Yates	51a0acd05b	Merge pull request #27 from genomic-medicine-sweden/add_nanopore ... Add nanopore reads preprocessing with Porechop	2022-03-21 19:41:58 +01:00
ljmesi	5b1b48e59e	Update subworkflow name to be more consistent	2022-03-21 18:29:47 +01:00
ljmesi	4940ec57ff	Remove unnecessary extra point	2022-03-21 18:26:26 +01:00
ljmesi	f6fe26de46	Rename shortread subworkflow to be more consistent	2022-03-21 18:25:56 +01:00
ljmesi	c97de32434	Make adapter and quality trimming optional	2022-03-21 18:17:08 +01:00