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Sofia Stamouli
18c15f8a78
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 20:23:38 +01:00
Sofia Stamouli
fb9de1e212
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 20:23:32 +01:00
Sofia Stamouli
8404c28d08
Review suggestion 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 20:23:26 +01:00
Sofia Stamouli
2e08c873a0
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 17:34:19 +01:00
Sofia Stamouli
0cbd0a8013
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 17:33:35 +01:00
Sofia Stamouli
af7468522a
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 17:33:18 +01:00
Sofia Stamouli
964771c5f2
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 17:33:04 +01:00
Sofia Stamouli
3c33ba66ca
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 17:32:13 +01:00
Sofia Stamouli
af8fd18d97
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 15:44:35 +01:00
Sofia Stamouli
b0a6bdee5a
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 15:43:45 +01:00
Sofia Stamouli
c6710db7a9
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 15:42:41 +01:00
Sofia Stamouli
d7c4554b18
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-20 15:42:10 +01:00
Sofia Stamouli
3eb6a29fb0
Merge branch 'nf-core:dev' into update_output 2022-12-20 15:30:19 +01:00
James Fellows Yates
11db981a88 minor fixes 2022-12-20 13:55:15 +01:00
Sofia Stamouli
c9e4eba62d Prettier 2022-12-13 11:26:06 +01:00
sofstam
4756dc7f0d Update output.md 2022-12-12 17:14:57 +01:00
sofstam
b1eb477f33 Update output.md 2022-12-12 17:06:05 +01:00
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
sofstam
b35d26744d Add classifiers 2022-12-09 17:11:48 +01:00
Sofia Stamouli
6d0b5d0a58 Prettier 2022-12-09 15:38:59 +01:00
sofstam
c5f4c9486a Start the documentation of output.md 2022-12-09 15:30:11 +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
Moritz E. Beber
4529e7e545 refactor: change parameter exclude unmerged to include 2022-12-04 21:36:12 +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
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
James Fellows Yates
f414f5dc9c Add falco to tube map 2022-11-04 18:20:44 +01:00
James Fellows Yates
4275640d9b update tubemap to include samtools stats 2022-11-04 15:24:15 +01:00
James Fellows Yates
6459d8920f Linting! 2022-11-03 14:05:43 +01:00
Mahwash Jamy
aecf308840 Update documentation for krakenuniq 2022-10-31 16:41:35 +00:00
Moritz E. Beber
bf89525bc2
Merge pull request #146 from nf-core/feat-bracken 
add Bracken to the profiling workflow
 2022-10-27 17:35:06 +02:00
Sofia Stamouli
8c3e80b6ea Add helptest to nextflow_schema,add versions to longread_preprocessing 2022-10-25 11:13:26 +02:00
nf-core-bot
00038db634 [automated] Fix linting with Prettier 2022-10-25 08:51:58 +00:00
Moritz E. Beber
ca7dc308cb
Apply suggestions from code review 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-10-21 16:36:35 +02:00
Moritz E. Beber
7bd6112133 docs: describe Bracken database usage 2022-10-21 10:18:11 +02:00
Sofia Stamouli
0481bb9449 Prettier 2022-10-18 17:48:40 +02:00
Sofia Stamouli
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +02:00
James A. Fellows Yates
4f27998852
Update usage.md 2022-10-14 14:37:52 +02:00
Sofia Stamouli
2423c9d87c
Add headers 2022-10-11 15:02:01 +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
Rafal Stepien
768f9980d8 Add pep_input_base_dir to workflow. Just need to update modules 2022-09-15 12:31:49 -04:00
Rafal Stepien
5f3eee9a4a Add working version of PEP-nf-core integration 2022-09-14 14:28:48 -04:00
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
Sofia Stamouli
c664508240
Update usage.md 2022-09-13 15:56:06 +02:00
James Fellows Yates
3a6536b149 Add tube map properly 2022-09-07 11:22:22 +02:00
James Fellows Yates
3eb136ec3c Merge branch 'dev' into json-schema 2022-08-31 12:55:49 +02:00
James A. Fellows Yates
28d8d3f8fb
Merge branch 'dev' into nf-core-template-merge-2.5 2022-08-31 09:16:34 +02:00