469 commits

This branch

This branch

All branches

Author	SHA1	Message	Date
Rafal Stepien	9349346864	Remove --pep parameter and leave just --input	2022-09-16 10:14:01 -04:00
Rafal Stepien	768f9980d8	Add pep_input_base_dir to workflow. Just need to update modules	2022-09-15 12:31:49 -04:00
Rafal Stepien	5f3eee9a4a	Add working version of PEP-nf-core integration	2022-09-14 14:28:48 -04:00
Sofia Stamouli	343a9e8d16	Merge pull request #131 from nf-core/FAQs_README ... Update usage.md	2022-09-14 09:00:17 +02:00
Sofia Stamouli	ded6d7ab1f	Update docs/usage.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-13 18:13:00 +02:00
Sofia Stamouli	0072c29a6f	Update docs/usage.md ... Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>	2022-09-13 18:12:14 +02:00
Sofia Stamouli	c664508240	Update usage.md	2022-09-13 15:56:06 +02:00
James A. Fellows Yates	db688575f6	Merge pull request #128 from nf-core/fastp-patch-removal ... use proper working FASTP module	2022-09-09 19:07:12 +02:00
James A. Fellows Yates	b28052f1ec	Remove patch from modules.json	2022-09-09 11:15:25 +02:00
James Fellows Yates	f087136ec9	use proper working FASTP module	2022-09-09 11:12:47 +02:00
James A. Fellows Yates	3fc7f1f0f8	Merge pull request #127 from nf-core/module-update ... Update all modules	2022-09-08 16:23:44 +02:00
James Fellows Yates	60224e9149	Patch fastp until I have an OK on the module update	2022-09-08 14:25:23 +02:00
James A. Fellows Yates	cc5df924e4	Merge branch 'dev' into module-update	2022-09-08 13:36:21 +02:00
James A. Fellows Yates	74c164bbcd	Merge pull request #126 from nf-core/kaiju2table-move ... Kaiju2table move	2022-09-08 13:21:27 +02:00
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