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Author SHA1 Message Date
Sofia Stamouli
5b99d9024a Add samtools stats for short-reads 2022-10-28 14:24:33 +02:00
Sofia Stamouli
f87131c7b1 Save samtools stats output 2022-10-28 14:10:24 +02:00
Sofia Stamouli
1bd6dbfe58 Add samtools stats for long-reads 2022-10-28 11:40:50 +02:00
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
James A. Fellows Yates
10f7f9e5de Merge branch 'adapterremoval-fix' of https://github.com/nf-core/taxprofiler into adapterremoval-fix 2022-10-27 12:23:52 +00:00
James A. Fellows Yates
08d61065e5 Add adapterlist to AR2 subworkflow 2022-10-27 12:23:27 +00:00
nf-core-bot
a402ee3be2 [automated] Fix linting with Prettier 2022-10-27 12:20:08 +00:00
James A. Fellows Yates
733d3dc8c5
Apply suggestions from code review 2022-10-27 14:19:28 +02:00
James A. Fellows Yates
76a662ecc5 Fix adapterremoval adapter conflict and add optional adapter list file 2022-10-27 12:17:19 +00:00
Moritz E. Beber
e658fab430 fix: remove def 
No idea why, must have something to do with scope.
 2022-10-27 11:50:47 +02:00
Moritz E. Beber
dd1a4ff158 refactor: only combine same database name 
[skip ci]
 2022-10-27 11:19:14 +02:00
Moritz E. Beber
0de1ac5356 docs: add Bracken reference 2022-10-27 10:14:57 +02:00
Sofia Stamouli
63c260bfbc
Merge pull request #148 from genomic-medicine-sweden/add_falco 
Add Falco as an alternative to FastQC
 2022-10-25 12:40:26 +02:00
Mahwash Jamy
f4717be9ab add krakenuniq to modules.config 2022-10-25 09:50:44 +00:00
Mahwash Jamy
86ca71cfd4 include krakenuniq in profiling subworkflow 2022-10-25 09:45:05 +00:00
Mahwash Jamy
36e101a78b Install krakenuniq module 2022-10-25 09:26:33 +00:00
Sofia Stamouli
de6816ec49
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-10-25 11:19:16 +02:00
Sofia Stamouli
7b1a53b062
Update nextflow_schema.json 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-10-25 11:19:08 +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
Sofia Stamouli
d3d4297ca9 Apply review suggestions 2022-10-24 16:28:07 +02:00
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
60e369aa5c fix: set default run bracken to false 2022-10-21 10:47:51 +02:00
Moritz E. Beber
7bd6112133 docs: describe Bracken database usage 2022-10-21 10:18:11 +02:00
Moritz E. Beber
385507ec6f refactor: use tool name 'bracken' only 2022-10-21 10:03:36 +02:00
Sofia Stamouli
19231538da Prettier 2022-10-20 16:59:32 +02:00
Sofia Stamouli
511cb16a61 Apply review suggestions 2022-10-20 16:55:57 +02:00
Moritz E. Beber
8deb7757d8 fix: remove Bracken from standardise reports 2022-10-19 16:21:57 +02:00
Moritz E. Beber
b73b479860 refactor: handle combined kraken2+bracken tool column 2022-10-19 16:21:36 +02:00
Moritz E. Beber
c7c7a7f678 refactor: change Bracken prefix to be more specific 2022-10-19 16:20:09 +02:00
Sofia Stamouli
7881ba9aef Fix the amount of left-padding spaces 2022-10-18 17:50:49 +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
Moritz E. Beber
8768a16d63 refactor: turn warning into error 2022-10-17 17:35:41 +02:00
Moritz E. Beber
48b00b7d62 refactor: create standardized Bracken reports 2022-10-17 17:33:24 +02:00
Moritz E. Beber
fd8a0df2a6 refactor: add warning when run_kraken2 is missing 2022-10-17 17:16:21 +02:00
Moritz E. Beber
563b34c9c3 refactor: rename process to kraken2 2022-10-14 14:48:27 +02:00
Moritz E. Beber
95621ebd8a fix: include local module 2022-10-14 14:47:08 +02:00
James A. Fellows Yates
4f27998852
Update usage.md 2022-10-14 14:37:52 +02:00
Moritz E. Beber
9dc819ceff style: reformat schema 2022-10-14 13:16:54 +02:00
Moritz E. Beber
c4f6468275 chore: update parameters schema 2022-10-14 12:55:26 +02:00
Moritz E. Beber
7f8180f458 fix: emit tool versions 2022-10-14 12:49:07 +02:00
Moritz E. Beber
767663d975 chore: add Bracken to test configs 2022-10-14 12:18:55 +02:00
Moritz E. Beber
ca38d002de feat: integrate Bracken into the profiling pipeline 2022-10-14 12:18:07 +02:00
Moritz E. Beber
4f728648f5 feat: add process to standardize kraken report 2022-10-14 10:56:14 +02:00
Moritz E. Beber
4352d35937 chore: install Bracken module 2022-10-14 10:52:17 +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
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