418 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
James Fellows Yates	acd0570b4a	Finalise first pass of nextflow json documentation	2022-08-31 07:56:39 +02:00
James Fellows Yates	bdcae4f934	More docs and tweat to usage.md	2022-08-30 16:04:05 +02:00
James Fellows Yates	c2eaa3f6b0	Prettier	2022-08-30 14:33:40 +02:00
James Fellows Yates	d19a473c59	Merge branch 'filtlong-in-tests' into json-schema	2022-08-30 14:33:19 +02:00
James A. Fellows Yates	f393d1fe91	Update nextflow.config	2022-08-30 14:21:20 +02:00
James Fellows Yates	5552c264b9	Remove now unnecessary input validation	2022-08-30 14:14:01 +02:00
James Fellows Yates	8917e29e35	Fix accidental overly zelous search-and-replace	2022-08-30 14:11:48 +02:00
James Fellows Yates	3f8f32cba8	Make longread quality ftilering opt out	2022-08-30 14:08:05 +02:00
James Fellows Yates	afba604e8b	Make everything within opt-out, once QC is opted-in	2022-08-30 14:04:34 +02:00
James Fellows Yates	95ad380173	Turn of length filtering by default for short read (to match opt in for longread qc)	2022-08-30 14:01:52 +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 Fellows Yates	d4af88e3ff	Make kaiju parameter clearer for documentation purpses and update documentation	2022-08-25 15:50:28 +02:00
James Fellows Yates	d6d51e0e43	Start work on reordering json schema parameters	2022-08-24 15:23:51 +02:00
James A. Fellows Yates	1821496a49	Merge pull request #90 from nf-core/samplesheet-check-improvement ... Make check_samplesheet.py compatible with nf-core/fetchngs	2022-08-23 15:57:59 +01:00
James A. Fellows Yates	22e03e73e3	Merge pull request #111 from nf-core/minimal-test ... Add test_nothing config profile for very minimal testing	2022-08-23 15:57:52 +01:00
James A. Fellows Yates	a3055bf6da	Update conf/test_nothing.config	2022-08-23 15:48:02 +02:00
James A. Fellows Yates	4315141c5f	Update bin/check_samplesheet.py ... Co-authored-by: Moritz E. Beber <midnighter@posteo.net>	2022-08-23 15:44:53 +02:00
James Fellows Yates	e6c7939305	Add test_nothing config profile for minimal testing	2022-08-23 14:37:01 +02:00
James Fellows Yates	a97bb69cd2	Prettier	2022-08-23 14:24:57 +02:00
James A. Fellows Yates	de70b0a01d	Merge pull request #109 from nf-core/centrifuge_mqc ... Trying to get Centrifuge output into MQC	2022-07-29 13:36:25 +02:00
James A. Fellows Yates	3e24f491b5	Merge pull request #106 from nf-core/porechop-log ... Add emitting porechop logs to multiqc and fix collection of others	2022-07-29 10:58:12 +02:00
James A. Fellows Yates	f48b22d615	Apply suggestions from code review	2022-07-29 09:52:49 +02:00
James Fellows Yates	873a13e028	Merge remote-tracking branch 'origin/dev' into porechop-log	2022-07-29 09:51:34 +02:00
Mahwash Jamy	06298e867c	Merge pull request #105 from genomic-medicine-sweden/diamond-update ... Update the dev branch with the DIAMOND module update	2022-07-28 17:21:59 +02:00
mjamy	5cdf5e958a	Updated modules.config to add 'log' in diamond config	2022-07-28 16:08:15 +02:00
Mahwash Jamy	49487593e2	Merge branch 'nf-core:dev' into diamond-update	2022-07-28 15:48:59 +02:00
Sofia Stamouli	ba928af5ab	Merge pull request #110 from genomic-medicine-sweden/update_centrifuge_kreport ... Update centrifuge kreport	2022-07-28 10:36:30 +02:00
sofstam	71cf32cc6a	Add error strategy for centrifuge/kreport	2022-07-28 08:54:32 +02:00
sofstam	9bc45a3f24	Update centrifuge/kreport	2022-07-27 14:44:26 +02:00
sofstam	cecbb41f88	Update centrifuge/kreport	2022-07-27 14:42:35 +02:00
James Fellows Yates	25bcc0798d	Start work on multiQC config with distinguishing Kraken/Centrifuge	2022-07-27 14:40:17 +02:00
nf-core-bot	a3bcf8665a	[automated] Fix linting with Prettier	2022-07-26 18:47:40 +00:00
James A. Fellows Yates	65ae82efc4	Define separte krakena nd centrigfue modules	2022-07-26 18:37:33 +00:00
James A. Fellows Yates	9d2be68fb8	Merge branch 'dev' into centrifuge_mqc	2022-07-26 18:01:30 +00:00
James A. Fellows Yates	1ef0975736	Merge branch 'dev' into porechop-log	2022-07-26 18:00:28 +00:00
James A. Fellows Yates	fdd9a3bc4d	Merge pull request #107 from nf-core/fix-multiqc-mixing ... Fix MultiQC mixing	2022-07-26 12:38:52 +02:00
James A. Fellows Yates	65b0af9a8b	Fix profiling channels	2022-07-26 08:53:43 +00:00
James A. Fellows Yates	3054dea7c2	Get multiqc input working	2022-07-26 08:41:06 +00:00
James A. Fellows Yates	e76b299705	Start working getting kraken and centrifuge working in MQC	2022-07-26 08:18:54 +00:00
James Fellows Yates	139cf0d6aa	Fix	2022-07-26 10:12:33 +02:00
James A. Fellows Yates	64f01fcfe0	Merge branch 'dev' into porechop-log	2022-07-20 14:05:23 +02:00
Sofia Stamouli	1fe9c133f1	Merge pull request #103 from genomic-medicine-sweden/update_filtlong ... Update the dev branch with the filtlong update	2022-07-20 10:44:52 +02:00
James Fellows Yates	255afee4c7	Re-add the collects	2022-07-19 17:10:10 +02:00
Mahwash Jamy	811ded38af	Update subworkflows/local/profiling.nf ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-07-19 16:44:48 +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
mjamy	c4c82212e1	incorporate diamond log file into multiqc channel	2022-07-19 14:12:16 +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