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Author SHA1 Message Date
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
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