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Author SHA1 Message Date
sofstam
c9a6320dac Merge branch 'update_output' of https://github.com/genomic-medicine-sweden/taxprofiler into update_output 
Conflicts:
	docs/output.md
 2022-12-12 09:13:02 +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
sofstam
b35d26744d Add classifiers 2022-12-09 17:11:48 +01:00
Sofia Stamouli
6d0b5d0a58 Prettier 2022-12-09 15:38:59 +01:00
Sofia Stamouli
98f3ab9fd1 Apply prettier 2022-12-09 15:35:51 +01:00
sofstam
c5f4c9486a Start the documentation of output.md 2022-12-09 15:30:11 +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
sofstam
6d140c683a Merge branch 'dev' into update_motus 2022-12-01 18:49:23 +01:00
James A. Fellows Yates
80c25008d0
Merge pull request #177 from nf-core/sep-krakenuniq-test 
Separate KrakenUniq test run
 2022-12-01 17:34:30 +01:00
nf-core-bot
410196c37b [automated] Fix linting with Prettier 2022-12-01 14:33:34 +00:00
sofstam
4800a5f03e Update schema 2022-12-01 14:23:40 +01:00
James A. Fellows Yates
a34b240dfc
Merge pull request #174 from nf-core/malt-update 
Update MALT
 2022-12-01 13:58:30 +01:00
James Fellows Yates
f960c14caf Fix typos 2022-12-01 13:46:57 +01:00
sofstam
38a818fd17 Apply review suggestions 2022-12-01 13:42:21 +01:00
James A. Fellows Yates
ef1d2da179
Apply suggestions from code review 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-12-01 12:53:34 +01:00
sofstam
1965ade961 Update schema 2022-12-01 11:32:51 +01:00
sofstam
e5bb627402 Apply review suggestions 2022-12-01 11:12:31 +01:00
James Fellows Yates
bc98f5b80f Separate KrakenUniq test run 2022-12-01 10:37:14 +01:00
nf-core-bot
8067012c01 [automated] Fix linting with Prettier 2022-12-01 09:15:35 +00:00
James A. Fellows Yates
4f6eb6fd75
Merge pull request #153 from mjamy/add-krakenuniq-module 
Add krakenuniq module
 2022-12-01 09:03:29 +01:00
sofstam
933b820c19 Apply review suggestions 2022-11-29 16:57:07 +01:00
Sofia Stamouli
e85c75dcba
Merge branch 'dev' into update_motus 2022-11-29 15:12:31 +01:00
sofstam
12dd836e9c Fix conflict 2022-11-29 15:00:27 +01:00