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529 commits 7 branches 0 tags 7.5 MiB
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110 commits

Author SHA1 Message Date
James A. Fellows Yates
76a662ecc5 Fix adapterremoval adapter conflict and add optional adapter list file 2022-10-27 12:17:19 +00:00
Sofia Stamouli
de6816ec49
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-10-25 11:19:16 +02:00
Sofia Stamouli
7b1a53b062
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-10-25 11:19:08 +02:00
Sofia Stamouli
8c3e80b6ea Add helptest to nextflow_schema,add versions to longread_preprocessing 2022-10-25 11:13:26 +02:00
Sofia Stamouli
19231538da Prettier 2022-10-20 16:59:32 +02:00
Sofia Stamouli
511cb16a61 Apply review suggestions 2022-10-20 16:55:57 +02:00
Sofia Stamouli
0481bb9449 Prettier 2022-10-18 17:48:40 +02:00
Sofia Stamouli
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +02:00
Moritz E. Beber
fdb8a7f740 Merge branch 'devel' into nf-core-template-merge-2.6 2022-10-05 12:21:54 +02:00
nf-core-bot
51bacb00e6 Template update for nf-core/tools version 2.6 2022-10-05 03:30:53 +00:00
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
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
9349346864 Remove --pep parameter and leave just --input 2022-09-16 10:14:01 -04:00
Rafal Stepien
5f3eee9a4a Add working version of PEP-nf-core integration 2022-09-14 14:28:48 -04:00
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
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 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
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 Fellows Yates
d8c0e9e7fe Prettier 2022-07-12 11:41:07 +02:00
James Fellows Yates
a0ee82bf43 Add motus/merge and biom support 2022-07-12 11:39:26 +02:00
James A. Fellows Yates
8082c7d108
Merge pull request #97 from nf-core/malt-to-krona 
Add Krona support for MALT
 2022-07-05 15:17:52 +02:00
James A. Fellows Yates
26e31c782d
Merge branch 'dev' into motus 2022-07-04 13:14:42 +02:00
James Fellows Yates
97e6cdf4b4 Add Krona taxonomy DB to schema build 2022-06-30 18:36:13 +02:00
James Fellows Yates
af854f5f34 Update mimetype for database csv as per https://github.com/nf-core/mag/pull/325/files 2022-06-28 12:42:41 +02:00
Thomas A. Christensen II
18284e6e32
Add run_krona option to allow skipping Krona chart creation 2022-06-27 08:45:08 -05:00
JIANHONG OU
c8a59adbce remove the database auto-download for mOTUs. 2022-06-03 14:13:58 -04:00
James Fellows Yates
3313b90453 Fix JSOn schema 2022-06-03 13:50:48 +02:00
James A. Fellows Yates
96fecb2bfc
Merge branch 'dev' into support-aligned-reads 2022-06-03 13:48:54 +02:00
James A. Fellows Yates
53c4399052
Merge branch 'dev' into motus 2022-06-02 21:38:35 +02:00
James Fellows Yates
2838c136bd Prettier 2022-06-02 12:51:39 +02:00
James A. Fellows Yates
c9581b1796
Merge branch 'dev' into support-aligned-reads 2022-06-02 12:45:29 +02:00
James Fellows Yates
d3d28da1b1 Update after review 2022-06-02 11:53:53 +02:00
James Fellows Yates
792e2d019b Fix merge error in schema 2022-05-31 13:06:48 +02:00
James Fellows Yates
310ac6b450 Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong 2022-05-31 13:05:52 +02:00
JIANHONG OU
68d0cc00fa add motus profile. 2022-05-23 08:05:06 -04:00
James Fellows Yates
0f651873dd Linting 2022-05-07 06:12:24 +02:00
James Fellows Yates
47a5ae0cff Add FASTP complexity option 2022-05-07 06:09:05 +02:00
James Fellows Yates
87a1d80519 Add working output for Kraken2/Centrifuge/DIAMOND 2022-05-07 05:22:35 +02:00
ljmesi
6618e8cac6 Change param to a more generic name 2022-05-05 13:20:34 +02:00
ljmesi
557d31dfd2 Add parameter for turning on longread host removal 2022-05-05 13:19:10 +02:00
ljmesi
d94534e8ac Simplify params which control host removal publish 2022-05-05 09:07:33 +02:00
ljmesi
c833d4fd9a Fix issues found with prettier 2022-05-03 11:42:05 +02:00
ljmesi
17039ebc6b Fix type to boolean for flags 2022-05-03 11:07:23 +02:00
ljmesi
fa1c132635 Update nextflow_schema 2022-05-03 11:03:25 +02:00