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Author SHA1 Message Date
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
James A. Fellows Yates
f43c54317c
Update subworkflows/local/standardisation_profiles.nf 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
 2022-09-16 15:20:47 +02:00
James Fellows Yates
63b3cc678f Merge branch 'motus-merge-meta' of github.com:nf-core/taxprofiler into motus-merge-meta 2022-09-16 10:25:28 +02:00
James Fellows Yates
c5cc21d29e Update motus merge module to remove unused channel 2022-09-16 10:25:24 +02:00
James A. Fellows Yates
2c83b367a7
Apply suggestions from code review 2022-09-16 09:28:42 +02:00
James Fellows Yates
4e7857e2ed Standardise mOTUs table merge 2022-09-16 08:36:34 +02:00
Rafal Stepien
768f9980d8 Add pep_input_base_dir to workflow. Just need to update modules 2022-09-15 12:31:49 -04:00
James A. Fellows Yates
cdb21d17b3
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-15 13:08:57 +02:00
James A. Fellows Yates
d9795a4fdc
Merge pull request #130 from nf-core/krakentools/combinekreports 
Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU
 2022-09-15 13:00:07 +02:00
James Fellows Yates
19a195ed14 Append profiler to resulting file 2022-09-15 12:30:39 +02:00
James Fellows Yates
21ae9d85c3 Ensure merge metaphlan3 tables happens on per database basis 2022-09-15 12:29:54 +02:00
James A. Fellows Yates
cd83c04c98
Merge pull request #135 from nf-core/dev-warning 
Update README.md
 2022-09-15 08:30:41 +02:00
James A. Fellows Yates
23a33a63cc
Update README.md 2022-09-15 08:11:37 +02:00
Rafal Stepien
5f3eee9a4a Add working version of PEP-nf-core integration 2022-09-14 14:28:48 -04:00
James A. Fellows Yates
5414ae2e55
Apply suggestions from code review 2022-09-14 11:20:40 +02:00
James Fellows Yates
abbbf9c7ab Update to use tar module compatible for our test databases 2022-09-14 11:16:28 +02:00
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
James Fellows Yates
05e9d92444 Add centrigue kreports 2022-09-13 16:47:19 +02:00
Sofia Stamouli
c664508240
Update usage.md 2022-09-13 15:56:06 +02:00
James Fellows Yates
c8dbf5be47 Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU 2022-09-13 15:47:28 +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 Fellows Yates
a764bc4807 Start works - need updated module though t have meta 2022-09-09 13:57:06 +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