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Author	SHA1	Message	Date
James Fellows Yates	55d7919fa7	Revert "Update ci.yml" ... This reverts commit 176a0a6280.	2022-09-02 11:48:57 +02:00
James Fellows Yates	c479714a5e	Revert "Update ci.yml" ... This reverts commit 61560cf065.	2022-09-02 11:48:49 +02:00
James Fellows Yates	8fe7f8bf4b	Revert "Fix final linting problems for template merge" ... This reverts commit e64b3f85a4.	2022-09-02 11:47:33 +02:00
James A. Fellows Yates	61560cf065	Update ci.yml	2022-09-02 10:12:27 +02:00
James A. Fellows Yates	176a0a6280	Update ci.yml	2022-09-02 10:06:20 +02:00
James A. Fellows Yates	e64b3f85a4	Fix final linting problems for template merge	2022-09-02 06:07:33 +00:00
James A. Fellows Yates	8fff741f85	Merge branch 'dev' into nf-core-template-merge-2.5.1	2022-09-01 16:26:45 +02:00
nf-core-bot	28045430d1	Template update for nf-core/tools version 2.5.1	2022-09-01 13:34:04 +00:00
James A. Fellows Yates	2ca837a4a3	Merge pull request #115 from nf-core/json-schema ... Add documentation for all parameters JSON schema (and other minor usage documentation tweaks)	2022-08-31 15:19:07 +02:00
James Fellows Yates	3eb136ec3c	Merge branch 'dev' into json-schema	2022-08-31 12:55:49 +02:00
James A. Fellows Yates	f7b7fd63a4	Merge pull request #114 from nf-core/nf-core-template-merge-2.5 ... Important! Template update for nf-core/tools v2.5	2022-08-31 10:28:14 +02:00
James A. Fellows Yates	394084a31b	Merge pull request #113 from nf-core/filtlong-in-tests ... Improve longread QC parameters	2022-08-31 09:36:12 +02:00
James A. Fellows Yates	5274ac57af	Update .prettierignore	2022-08-31 09:24:24 +02:00
James A. Fellows Yates	28d8d3f8fb	Merge branch 'dev' into nf-core-template-merge-2.5	2022-08-31 09:16:34 +02:00
James Fellows Yates	0107330d92	Clarify specifying output parameters in database db_params column	2022-08-31 08:34:57 +02:00
James Fellows Yates	806208c4b1	Final tweaks to schema, and add a couple of notes for dev guidance on where their various --save_reads parameters are injected	2022-08-31 08:30:26 +02:00
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
nf-core-bot	6dfca81761	Template update for nf-core/tools version 2.5	2022-08-30 13:43:03 +00:00
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