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655 commits 7 branches 0 tags 7.5 MiB
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132 commits

Author SHA1 Message Date
sofstam
6d140c683a Merge branch 'dev' into update_motus 2022-12-01 18:49:23 +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
sofstam
38a818fd17 Apply review suggestions 2022-12-01 13:42:21 +01:00
sofstam
e5bb627402 Apply review suggestions 2022-12-01 11:12:31 +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
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 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
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
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
James Fellows Yates
4e7857e2ed Standardise mOTUs table merge 2022-09-16 08:36:34 +02:00
James A. Fellows Yates
cdb21d17b3
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-15 13:08:57 +02:00
James Fellows Yates
19a195ed14 Append profiler to resulting file 2022-09-15 12:30:39 +02:00
James Fellows Yates
05e9d92444 Add centrigue kreports 2022-09-13 16:47:19 +02:00
James Fellows Yates
c8dbf5be47 Adds KRAKEN_COMBINEKREPORTS for 'native' multi-sample OTU 2022-09-13 15:47:28 +02:00
James Fellows Yates
a764bc4807 Start works - need updated module though t have meta 2022-09-09 13:57:06 +02:00
James Fellows Yates
832d981976 Don't have per sample directory as unnecessary if file names are unique with the db in them 2022-09-07 12:22:17 +02:00
James Fellows Yates
7c5f9d0c24 Start work on more merging tools 2022-09-06 17:34:45 +02:00
James A. Fellows Yates
13e9957e14 Fixes process selector warning 2022-09-02 06:03:05 +00:00
James Fellows Yates
2cc07183a0 Standardise QC parameter system and turn on both porechop/filtlong in tests 2022-08-30 13:58:58 +02:00
James Fellows Yates
a97bb69cd2 Prettier 2022-08-23 14:24:57 +02:00
James A. Fellows Yates
de70b0a01d
Merge pull request #109 from nf-core/centrifuge_mqc 
Trying to get Centrifuge output into MQC
 2022-07-29 13:36:25 +02:00