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
|
35b7fc26f7
|
[skip ci]
|
2022-10-11 17:01:08 +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 |
|
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 |
|