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Author SHA1 Message Date
James A. Fellows Yates
44146b8fe3
Apply suggestions from code review 2022-09-30 08:34:53 +02:00
James A. Fellows Yates
8b559fba86 Pin version to get NXF to download correctly 2022-09-29 13:31:02 -04:00
Rafal Stepien
04d28e6520 Merge branch 'nf-core-add-pep-support' into add-pep-support 2022-09-28 14:51:38 -04:00
Rafal Stepien
00aa94a403 Merge branch 'add-pep-support' of github.com:nf-core/taxprofiler into nf-core-add-pep-support 2022-09-28 14:51:13 -04:00
Rafal Stepien
bfd260e9c8 Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-28 12:40:43 -04:00
James Fellows Yates
87edc4569c Move to a function 2022-09-27 15:46:17 +02:00
James Fellows Yates
43a8aa4405 Remove detect_reads.py and replace remaining checks with nextflow code instead 2022-09-27 15:32:51 +02:00
Rafal Stepien
1584d6fc51 Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-19 10:43:04 -04:00
Rafal Stepien
0ccbf50938
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-19 09:49:37 -04:00
Rafal Stepien
5b6c18f0a2
Update nextflow.config 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-19 09:49:28 -04:00
Rafal Stepien
e84b64f7e1
Update modules/local/samplesheet_check.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-19 09:49:20 -04:00
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