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Author SHA1 Message Date
Moritz E. Beber
8768a16d63 refactor: turn warning into error 2022-10-17 17:35:41 +02:00
Moritz E. Beber
48b00b7d62 refactor: create standardized Bracken reports 2022-10-17 17:33:24 +02:00
Moritz E. Beber
fd8a0df2a6 refactor: add warning when run_kraken2 is missing 2022-10-17 17:16:21 +02:00
Moritz E. Beber
563b34c9c3 refactor: rename process to kraken2 2022-10-14 14:48:27 +02:00
Moritz E. Beber
95621ebd8a fix: include local module 2022-10-14 14:47:08 +02:00
James A. Fellows Yates
4f27998852
Update usage.md 2022-10-14 14:37:52 +02:00
Moritz E. Beber
9dc819ceff style: reformat schema 2022-10-14 13:16:54 +02:00
Moritz E. Beber
c4f6468275 chore: update parameters schema 2022-10-14 12:55:26 +02:00
Moritz E. Beber
7f8180f458 fix: emit tool versions 2022-10-14 12:49:07 +02:00
Moritz E. Beber
767663d975 chore: add Bracken to test configs 2022-10-14 12:18:55 +02:00
Moritz E. Beber
ca38d002de feat: integrate Bracken into the profiling pipeline 2022-10-14 12:18:07 +02:00
Moritz E. Beber
4f728648f5 feat: add process to standardize kraken report 2022-10-14 10:56:14 +02:00
Moritz E. Beber
4352d35937 chore: install Bracken module 2022-10-14 10:52:17 +02:00
Sofia Stamouli
e98cd038c7
[skip ci] 
Add description for MALT
 2022-10-12 12:56:54 +02:00
Sofia Stamouli
0b16010b92
Add tutorials section 2022-10-12 11:39:03 +02:00
Sofia Stamouli
4e771ab2c7
Merge pull request #142 from genomic-medicine-sweden/update_readme 
Add KrakenUniq and Filtlong in documentation
 2022-10-12 11:38:01 +02:00
Sofia Stamouli
bd56bc0ed6
Add minimap2 and update contributors 2022-10-12 11:10:53 +02:00
Sofia Stamouli
d09a8e0545
[skip ci] 2022-10-11 17:44:48 +02:00
Sofia Stamouli
17b2ad3199 Add prettier 2022-10-11 17:29:41 +02:00
Sofia Stamouli
35b7fc26f7
[skip ci] 2022-10-11 17:01:08 +02:00
Sofia Stamouli
f22cf0c921
Update usage.md 2022-10-11 16:41:44 +02:00
Sofia Stamouli
f24344c168
Update README.md 2022-10-11 16:30:42 +02:00
Sofia Stamouli
2423c9d87c
Add headers 2022-10-11 15:02:01 +02:00
Sofia Stamouli
dea45c66c2
Add Krona description 2022-10-11 14:59:48 +02:00
James A. Fellows Yates
f25ee17fcf
Merge pull request #141 from nf-core/minimap-patch 
Remove necessity of patch
 2022-10-11 12:46:26 +02:00
James Fellows Yates
56bae85755 Remove necessity of patch 2022-10-11 12:38:18 +02:00
Sofia Stamouli
58dffc0c5d
Add KrakenUniq and Filtlong in documentation 2022-10-11 12:36:48 +02:00
James A. Fellows Yates
ff1670169a
Merge pull request #138 from nf-core/nf-core-template-merge-2.6 
Important! Template update for nf-core/tools v2.6
 2022-10-06 13:03:45 +02:00
Moritz E. Beber
5f3dbd28de fix: patch inputs to correspond to previous version 2022-10-05 13:51:15 +02:00
Moritz E. Beber
180cac0395 fix: adapt to new samtools/view input 2022-10-05 13:49:35 +02:00
Moritz E. Beber
f5af9fd939 fix: adjust import paths to re-organization 2022-10-05 13:40:43 +02:00
Moritz E. Beber
b407fbcdce chore: force update all modules 2022-10-05 12:24:18 +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
James A. Fellows Yates
3ca9058b9c
Merge pull request #133 from rafalstepien/add-pep-support 
Add working version of PEP-nf-core integration
 2022-09-30 10:21:15 +02:00
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
James A. Fellows Yates
187946ec80
Merge pull request #136 from nf-core/metaphlan3/mergemetaphlantables 
Add MetaPhlAn3 per-database multi-sample taxon tables
 2022-09-19 13:45:50 +02:00
Rafal Stepien
9349346864 Remove --pep parameter and leave just --input 2022-09-16 10:14:01 -04:00
James A. Fellows Yates
016efcb807
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-16 16:02:38 +02:00
James A. Fellows Yates
a2a9f458ec
Merge pull request #137 from nf-core/motus-merge-meta 
Standardise mOTUs table merge
 2022-09-16 16:01:38 +02:00