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Author SHA1 Message Date
James Fellows Yates
9e6a91aff9 Distinguish Kraken2 from Bracken 2022-12-15 13:25:01 +01:00
James Fellows Yates
3b86a22556 Fix falco publication names 2022-12-15 12:57:49 +01:00
James Fellows Yates
88589fbc53 Fix publishing of log files of rpreprocessing steps 2022-12-15 10:35:06 +01:00
Sofia Stamouli
644c4ab831 Review suggestions 2022-12-13 12:00:32 +01:00
Sofia Stamouli
3282f5944b Apply prettier 2022-12-13 11:28:17 +01:00
sofstam
d99706f43d Move database section and alphabetical order 2022-12-13 11:23:07 +01:00
Sofia Stamouli
f80adee9e2 Review suggestions and prettier 2022-12-13 09:50:05 +01:00
Sofia Stamouli
1eb3da758b
Apply review suggestion 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-13 09:38:09 +01:00
Sofia Stamouli
97e48075c8
Apply review suggestion 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-13 09:37:43 +01:00
James A. Fellows Yates
578081df2e
Merge pull request #189 from nf-core/database-check 
Adds (native groovy!) database check
 2022-12-13 08:43:00 +01:00
James A. Fellows Yates
971f6a6ea8
Merge pull request #190 from nf-core/motus-update-version 
Update mOTUs to 3.0.3
 2022-12-12 18:24:05 +01:00
Sofia Stamouli
a99f89af77 Apply review suggestions 2022-12-12 16:30:28 +01:00
James Fellows Yates
e31e7d3172 Update mOTUs to 3.0.3 2022-12-12 15:42:01 +01:00
Sofia Stamouli
bd5cd0a897 Prettier 2022-12-12 13:34:53 +01:00
sofstam
896a39e68d Apply review suggestions 2022-12-12 13:19:59 +01:00
James A. Fellows Yates
be85cb408c
Merge pull request #188 from nf-core/bracken-mergetables 
Add Bracken mergetables
 2022-12-12 11:26:19 +01:00
James Fellows Yates
7c66968fef More comments 2022-12-12 11:04:21 +01:00
James Fellows Yates
460f3ca157 Add database sheet validation 2022-12-12 11:03:40 +01:00
James Fellows Yates
3df0a383da Update combine bracken outputs to include meta for publishing purposes 2022-12-12 10:10:24 +01:00
James Fellows Yates
07bd989bc6 Start work on groovy native datbase checks 2022-12-12 10:02:22 +01:00
James Fellows Yates
4b68e95770 Revert PEP validation back to python samplesheet check 2022-12-12 08:49:13 +01:00
James Fellows Yates
8939ce3e20 Start adding bracken/combinebrackenreports (need smodule update) 2022-12-11 16:52:34 +01:00
Sofia Stamouli
98f3ab9fd1 Apply prettier 2022-12-09 15:35:51 +01:00
Sofia Stamouli
a622dcaef0
Delete one line 2022-12-09 13:59:37 +01:00
sofstam
5373c58331 Merge branch 'dev' into update_usage 2022-12-09 13:05:42 +01:00
sofstam
97fbc2bceb Update usage.md 2022-12-09 12:58:51 +01:00
James A. Fellows Yates
13c4f44ca6
Merge pull request #185 from nf-core/nf-core-template-merge-2.7.1 
Important! Template update for nf-core/tools v2.7.1
 2022-12-09 12:58:28 +01:00
sofstam
f0846ef213 Merge branch 'update_usage' of https://github.com/genomic-medicine-sweden/taxprofiler into update_usage 2022-12-09 10:38:03 +01:00
sofstam
3af71d9c63 Merge branch 'dev' into update_usage 2022-12-09 10:35:12 +01:00
James Fellows Yates
dca0b86c78 Fix versions 2022-12-09 10:28:48 +01:00
James Fellows Yates
da3d2d96e6 Fix linting 2022-12-09 10:27:50 +01:00
James Fellows Yates
1ccd0a0767 Merge branch 'dev' into nf-core-template-merge-2.7.1 2022-12-09 10:16:17 +01:00
nf-core-bot
36f3b5723b Template update for nf-core/tools version 2.7.1 2022-12-08 13:18:23 +00:00
James A. Fellows Yates
1687b43596
Merge pull request #183 from nf-core/update-bracken-params 
Update bracken so parameters come directly from database args
 2022-12-07 16:39:52 +01:00
James Fellows Yates
d8751787ac Update bracken so parameters come directly from database args 2022-12-07 07:27:40 +01:00
Sofia Stamouli
50da3d3efb
Merge branch 'nf-core:dev' into update_usage 2022-12-06 17:13:17 +01:00
James Fellows Yates
3dba6405c5 Sets correct default for --shortread_qc_mergepairs 2022-12-06 11:47:16 +01:00
Moritz E. Beber
9064584356
Merge pull request #180 from nf-core/rename-exclude-unmerged 
refactor: change parameter exclude unmerged to include
 2022-12-05 10:53:32 +01:00
Moritz E. Beber
24e5bc5410 refactor: use shorter and more explicit syntax 2022-12-04 21:54:10 +01:00
Moritz E. Beber
b2088bcbb3 docs: improve description of shortread_qc_includeunmerged 2022-12-04 21:53:38 +01:00
Moritz E. Beber
4529e7e545 refactor: change parameter exclude unmerged to include 2022-12-04 21:36:12 +01:00
James A. Fellows Yates
7992edd181
Merge pull request #181 from nf-core/sep-krakenuniq-test 
Filter out Nanopore reads from Bracken
 2022-12-04 13:57:11 +01:00
James Fellows Yates
0a0dffa37c Try separating MALT 2022-12-04 12:06:33 +01:00
James Fellows Yates
0dccfddc24 Switch order back 2022-12-03 21:38:25 +01:00
James A. Fellows Yates
cf8ad96771
Update subworkflows/local/profiling.nf 2022-12-02 15:09:08 +01:00
James Fellows Yates
ab42f6b662 wteak message 2022-12-02 12:49:00 +01:00
James Fellows Yates
a3cd188b1f Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test 2022-12-02 12:48:18 +01:00
James Fellows Yates
de74e4f727 Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md 2022-12-02 12:47:14 +01:00
Sofia Stamouli
c56c6ea694
Merge pull request #176 from nf-core/update_motus 
Include NCBI taxid, read counts and mgc arguments in motus
 2022-12-02 12:18:58 +01:00
Sofia Stamouli
7e7299203c
Set values to false 2022-12-02 08:55:23 +01:00