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Sofia Stamouli
5d12785ca4
Merge branch 'nf-core:dev' into update_output 2023-01-25 09:47:30 +01:00
James A. Fellows Yates
9cf2d8763f
[skip ci] Update docs/usage.md 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
 2023-01-24 11:50:58 +01:00
James Fellows Yates
085d9e519c [skip ci] add comment about recommendation to split SR/LR 2023-01-24 11:39:37 +01:00
Sofia Stamouli
7d4035d4c7
Add new line in the description of custom file 2023-01-19 13:44:10 +01:00
James A. Fellows Yates
36629b3dde
Merge branch 'dev' into post-usage-draft-tweaks 2023-01-19 10:36:59 +01:00
James A. Fellows Yates
6e43695264
Apply suggestions from code review 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
 2023-01-19 08:55:23 +01:00
James A. Fellows Yates
6d380fbbff
Apply suggestions from code review 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
 2023-01-19 08:49:55 +01:00
Sofia Stamouli
4dcf8c0b02 Prettier 2023-01-17 15:50:10 +01:00
sofstam
024b683671 Update output and usage 2023-01-17 15:38:56 +01:00
James Fellows Yates
33d4a84237 Add explicit sentnece about classification/profiling 2023-01-17 15:23:59 +01:00
nf-core-bot
11400b016c [automated] Fix linting with Prettier 2023-01-16 14:11:18 +00:00
James A. Fellows Yates
b34a021db7
Specify the difference between classification/profiling 2023-01-16 14:43:46 +01:00
Sofia Stamouli
06575b537d
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-01-16 12:59:23 +01:00
Sofia Stamouli
0e3f9f0b9a
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-01-16 12:59:13 +01:00
sofstam
9f21181972 Add documentation for output docs 2023-01-12 15:47:29 +01:00
Sofia Stamouli
3b6be07623
Merge branch 'nf-core:dev' into update_output 2023-01-11 16:56:18 +01:00
Sofia Stamouli
33bce738f5
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-01-11 16:50:06 +01:00
Sofia Stamouli
a49a907ad1
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-01-11 16:47:44 +01:00
Sofia Stamouli
953f9585c9
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-01-11 16:47:18 +01:00
Sofia Stamouli
719fc3cf5d
Update docs/output.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2023-01-11 16:46:30 +01:00
James Fellows Yates
ab0c62bdc1 Post-release tweaks to usage.md 2022-12-23 16:23:29 +01:00
Sofia Stamouli
ec9c7cfedc Prettier 2022-12-22 11:10:54 +01:00
Sofia Stamouli
2f291731c1
Merge branch 'nf-core:dev' into update_usage 2022-12-22 11:09:50 +01:00
Sofia Stamouli
1eeb3b337a
Update usage.md 2022-12-22 11:07:09 +01:00
Sofia Stamouli
29978d83b9
Update centrifuge section 2022-12-22 11:03:49 +01:00
Sofia Stamouli
d6e0d404e3
Update docs/usage.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-22 09:18:00 +01:00
Sofia Stamouli
ba43b0daa4
Update docs/usage.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-21 09:26:38 +01:00
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 
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 2022-12-20 20:23:26 +01:00
Sofia Stamouli
2e08c873a0
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 2022-12-20 17:34:19 +01:00
Sofia Stamouli
0cbd0a8013
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 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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 2022-12-20 15:43:45 +01:00
Sofia Stamouli
c6710db7a9
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 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
Sofia Stamouli
7be3cfc450 Review suggestions 2022-12-20 15:00:17 +01:00
James Fellows Yates
11db981a88 minor fixes 2022-12-20 13:55:15 +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
Sofia Stamouli
c9e4eba62d Prettier 2022-12-13 11:26:06 +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
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-13 09:38:09 +01:00
Sofia Stamouli
97e48075c8
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Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-12-13 09:37:43 +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
Sofia Stamouli
a99f89af77 Apply review suggestions 2022-12-12 16:30:28 +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
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
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
sofstam
3af71d9c63 Merge branch 'dev' into update_usage 2022-12-09 10:35:12 +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
e98cd038c7
[skip ci] 
Add description for MALT
 2022-10-12 12:56:54 +02:00
Sofia Stamouli
0b16010b92
Add tutorials section 2022-10-12 11:39:03 +02:00
Sofia Stamouli
d09a8e0545
[skip ci] 2022-10-11 17:44:48 +02:00
Sofia Stamouli
17b2ad3199 Add prettier 2022-10-11 17:29:41 +02:00
Sofia Stamouli
f22cf0c921
Update usage.md 2022-10-11 16:41:44 +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
James Fellows Yates
0107330d92 Clarify specifying output parameters in database db_params column 2022-08-31 08:34:57 +02:00
James Fellows Yates
bdcae4f934 More docs and tweat to usage.md 2022-08-30 16:04:05 +02:00
nf-core-bot
6dfca81761 Template update for nf-core/tools version 2.5 2022-08-30 13:43:03 +00:00