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181 commits

Author SHA1 Message Date
James Fellows Yates
0a0dffa37c Try separating MALT 2022-12-04 12:06:33 +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
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
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
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
James Fellows Yates
d7fbe55849 Add KU to the test profiles and add id to KU processes 2022-11-29 14:19:01 +01:00
Sofia Stamouli
7e3ece53bd
Update modules.config 2022-11-29 13:31:00 +01:00
Sofia Stamouli
0088b07220
Fix trailing whitespace 2022-11-29 13:28:04 +01:00
James A. Fellows Yates
770a35d7ac
Update conf/modules.config 2022-11-29 12:49:20 +01:00
Sofia Stamouli
ba727a81ae Fix left-padding spaces 2022-11-29 12:45:14 +01:00
Sofia Stamouli
71b52b9c94 Apply review suggestions 2022-11-29 11:58:23 +01:00
sofstam
49af33f68e Include NCBI_id, read counts and mgc arguments in motus 2022-11-29 11:07:29 +01:00
James A. Fellows Yates
f114cc4122
Apply suggestions from code review 2022-11-24 16:55:19 +01:00
James A. Fellows Yates
17b1e3df1c
Update test.config 2022-11-24 16:53:39 +01:00
James Fellows Yates
a20b3e3c58 Try to reduce MALT memory 2022-11-24 15:51:12 +01:00
James Fellows Yates
9feb6c2db6 Update MALT 2022-11-24 14:44:04 +01:00
Sofia Stamouli
d2195e9eda
Merge branch 'dev' into short_reads_samtools 2022-11-04 11:47:36 +01:00
Sofia Stamouli
b5e6639f9d
Apply review suggestions 2022-11-03 14:12:05 +01:00
James A. Fellows Yates
bc671c547d
Merge pull request #165 from genomic-medicine-sweden/fix_porechop_conflict
Fix porechop conflict
2022-11-03 14:08:13 +01:00
James A. Fellows Yates
1f31f88635
Merge pull request #158 from nf-core/adapterremoval-fix
Fix adapterremoval adapter conflict and add optional adapter list file
2022-11-03 11:36:14 +01:00
James Fellows Yates
d487a1ff2f Addd FASTP adadapter list 2022-11-02 12:39:34 +01:00
Sofia Stamouli
e4307ad8ab Change modules.config to include porechop_porechop 2022-11-01 20:50:42 +01:00
Mahwash Jamy
febcbfc057 add missing parameters to nextflow.config 2022-10-31 16:07:53 +00:00
Mahwash Jamy
3147a80a56 Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module 2022-10-31 15:36:57 +00:00
Sofia Stamouli
0e0c55d3b0
Update modules.config 2022-10-31 12:35:51 +01:00
Sofia Stamouli
a4b5fa9f57
Fix trailing space 2022-10-31 12:17:49 +01:00
Sofia Stamouli
1d1047374b
Fix EditorConfig format 2022-10-31 12:09:25 +01:00
Sofia Stamouli
c4a7d094c8 Fix EditorConfig check 2022-10-28 14:33:44 +02:00
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
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
76a662ecc5 Fix adapterremoval adapter conflict and add optional adapter list file 2022-10-27 12:17:19 +00:00
Mahwash Jamy
f4717be9ab add krakenuniq to modules.config 2022-10-25 09:50:44 +00:00
Moritz E. Beber
60e369aa5c fix: set default run bracken to false 2022-10-21 10:47:51 +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
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +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
James A. Fellows Yates
3ca9058b9c
Merge pull request #133 from rafalstepien/add-pep-support
Add working version of PEP-nf-core integration
2022-09-30 10:21:15 +02:00
James Fellows Yates
43a8aa4405 Remove detect_reads.py and replace remaining checks with nextflow code instead 2022-09-27 15:32:51 +02:00
Rafal Stepien
9349346864 Remove --pep parameter and leave just --input 2022-09-16 10:14:01 -04:00
James A. Fellows Yates
016efcb807
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-16 16:02:38 +02:00