28 commits

Author	SHA1	Message	Date
Moritz E. Beber	7104b12e3b	Update subworkflows/local/longread_preprocessing.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2023-03-11 11:28:42 +01:00
Moritz E. Beber	07db3c93e2	style: use map addition instead of cloning	2023-03-11 11:28:42 +01:00
Sofia Stamouli	3faea8aac5	Fix porechop conflict	2022-11-01 17:34:37 +01:00
Sofia Stamouli	8c3e80b6ea	Add helptest to nextflow_schema,add versions to longread_preprocessing	2022-10-25 11:13:26 +02:00
Sofia Stamouli	511cb16a61	Apply review suggestions	2022-10-20 16:55:57 +02:00
Sofia Stamouli	8eddb32b88	Add Falco as an alternative to FastQC	2022-10-18 17:43:16 +02:00
Moritz E. Beber	f5af9fd939	fix: adjust import paths to re-organization	2022-10-05 13:40:43 +02:00
James Fellows Yates	3f8f32cba8	Make longread quality ftilering opt out	2022-08-30 14:08:05 +02:00
James Fellows Yates	2cc07183a0	Standardise QC parameter system and turn on both porechop/filtlong in tests	2022-08-30 13:58:58 +02:00
James A. Fellows Yates	f48b22d615	Apply suggestions from code review	2022-07-29 09:52:49 +02:00
James A. Fellows Yates	64f01fcfe0	Merge branch 'dev' into porechop-log	2022-07-20 14:05:23 +02:00
James Fellows Yates	255afee4c7	Re-add the collects	2022-07-19 17:10:10 +02:00
Sofia Stamouli	237e9aa623	Update longread_preprocessing.nf	2022-07-19 16:44:08 +02:00
James A. Fellows Yates	8d7ddb5847	Apply suggestions from code review	2022-07-19 16:30:13 +02:00
sofstam	171258d545	Fix typos	2022-07-19 14:07:13 +02:00
sofstam	25bc01f9c4	Fix typos	2022-07-19 14:04:49 +02:00
sofstam	8147dba0b4	Fix typos	2022-07-19 14:03:10 +02:00
sofstam	526ed79763	Fix filtlong logs	2022-07-19 14:01:11 +02:00
sofstam	1ba6a08135	Seperate multiqc for filtlong	2022-07-19 13:53:29 +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	5a2fd260fd	Log file into multiqc channel	2022-07-15 12:50:50 +02:00
James Fellows Yates	9462032d00	Fix MALT save_alignemnts reads and some clean up	2022-06-03 22:29:04 +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	b055df5ea0	Add bbduk complexity (entropy-based) filtering	2022-04-02 17:02:05 +02:00
James Fellows Yates	93aaa9eeac	Clean up AdapterRemoval and remove all debugging dumps	2022-04-01 21:36:22 +02:00
James Fellows Yates	ede362dbf9	Remove duplicate config and sync longread fastqc	2022-03-25 15:28:30 +01:00
James Fellows Yates	b5f5c75504	Fix file header descriptions	2022-03-25 15:21:52 +01:00
ljmesi	1e42f1d9f2	Add long read preprocessing subworkflow	2022-03-18 15:10:44 +01:00