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Author	SHA1	Message	Date
James Fellows Yates	fc26948950	Fix MultiQC	2022-09-08 12:49:38 +02:00
James Fellows Yates	d11257b330	Module update	2022-09-08 08:08:36 +02:00
James Fellows Yates	bbd8049ca1	Remove duplicated multqic mixing	2022-09-07 13:44:08 +02:00
James A. Fellows Yates	6f87c681fd	Merge pull request #125 from nf-core/workflow-tube-map ... Workflow tube map	2022-09-07 12:52:38 +02:00
James Fellows Yates	832d981976	Don't have per sample directory as unnecessary if file names are unique with the db in them	2022-09-07 12:22:17 +02:00
James Fellows Yates	3a6536b149	Add tube map properly	2022-09-07 11:22:22 +02:00
James Fellows Yates	175be0075a	Add tube map	2022-09-07 11:22:06 +02:00
James Fellows Yates	7c5f9d0c24	Start work on more merging tools	2022-09-06 17:34:45 +02:00
James A. Fellows Yates	8c6f88d1b5	Merge pull request #118 from nf-core/motus-test-fix ... Fix mOTUs CI and old param warn	2022-09-05 10:38:58 +02:00
James A. Fellows Yates	dd194f3f47	Fix mOTUs CI and old param warn	2022-09-04 15:01:58 +00:00
James A. Fellows Yates	d093de1bd0	Merge pull request #117 from nf-core/fix-selector-warns ... Fixes process selector warning	2022-09-04 16:23:53 +02:00
James A. Fellows Yates	331231ea28	Standardise CI execution	2022-09-04 14:02:54 +00:00
James A. Fellows Yates	8456f934ed	Update subworkflows/local/visualization_krona.nf	2022-09-02 16:15:46 +02:00
James Fellows Yates	ef6fd002d4	Merge branch 'dev' into fix-selector-warns	2022-09-02 14:11:03 +02:00
James A. Fellows Yates	c9a7797682	Merge pull request #116 from nf-core/nf-core-template-merge-2.5.1 ... Important! Template update for nf-core/tools v2.5.1	2022-09-02 13:47:39 +02:00
James Fellows Yates	c3427e44b3	Try with retries from sarek approach	2022-09-02 12:24:29 +02:00
James Fellows Yates	3a33d81e80	Black linting I hope	2022-09-02 11:55:19 +02:00
James Fellows Yates	7917e1d656	Synronise mOTUs CI setup	2022-09-02 11:51:18 +02:00
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	13e9957e14	Fixes process selector warning	2022-09-02 06:03:05 +00:00
James A. Fellows Yates	169c7437c8	Left over from template merge	2022-09-01 16:28:05 +02:00
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