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120 commits

Author SHA1 Message Date
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 A. Fellows Yates
4f6eb6fd75
Merge pull request #153 from mjamy/add-krakenuniq-module
Add krakenuniq module
2022-12-01 09:03:29 +01:00
Moritz E. Beber
af8ce2cbfd chore: update krakenuniq 2022-11-29 10:27:35 +01:00
James Fellows Yates
131b39aa8b Fix linting 2022-11-24 15:49:06 +01:00
James Fellows Yates
9feb6c2db6 Update MALT 2022-11-24 14:44:04 +01:00
James Fellows Yates
a383c9ae40 Remove the join 2022-11-22 13:39:21 +01:00
James Fellows Yates
cacd7d3128 Not just in stub 2022-11-22 13:33:13 +01:00
James Fellows Yates
e8de006ed6 With a join 2022-11-22 13:27:49 +01:00
James Fellows Yates
ebfc84e235 Does the grouping work if we have meta? 2022-11-22 13:26:54 +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
3faea8aac5 Fix porechop conflict 2022-11-01 17:34:37 +01:00
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
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
76a662ecc5 Fix adapterremoval adapter conflict and add optional adapter list file 2022-10-27 12:17:19 +00:00
Mahwash Jamy
36e101a78b Install krakenuniq module 2022-10-25 09:26:33 +00:00
Sofia Stamouli
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +02:00
Moritz E. Beber
563b34c9c3 refactor: rename process to kraken2 2022-10-14 14:48:27 +02:00
Moritz E. Beber
7f8180f458 fix: emit tool versions 2022-10-14 12:49:07 +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
James Fellows Yates
56bae85755 Remove necessity of patch 2022-10-11 12:38:18 +02:00
Moritz E. Beber
5f3dbd28de fix: patch inputs to correspond to previous version 2022-10-05 13:51:15 +02:00
Moritz E. Beber
b407fbcdce chore: force update all modules 2022-10-05 12:24:18 +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
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
e84b64f7e1
Update modules/local/samplesheet_check.nf
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
2022-09-19 09:49:20 -04:00
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
c5cc21d29e Update motus merge module to remove unused channel 2022-09-16 10:25:24 +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
21ae9d85c3 Ensure merge metaphlan3 tables happens on per database basis 2022-09-15 12:29:54 +02:00
Rafal Stepien
5f3eee9a4a Add working version of PEP-nf-core integration 2022-09-14 14:28:48 -04:00
James Fellows Yates
abbbf9c7ab Update to use tar module compatible for our test databases 2022-09-14 11:16:28 +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
f087136ec9 use proper working FASTP module 2022-09-09 11:12:47 +02:00
James Fellows Yates
60224e9149 Patch fastp until I have an OK on the module update 2022-09-08 14:25:23 +02:00
James Fellows Yates
fc26948950 Fix MultiQC 2022-09-08 12:49:38 +02:00
James Fellows Yates
d11257b330 Module update 2022-09-08 08:08:36 +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
nf-core-bot
6dfca81761 Template update for nf-core/tools version 2.5 2022-08-30 13:43:03 +00:00
James Fellows Yates
873a13e028 Merge remote-tracking branch 'origin/dev' into porechop-log 2022-07-29 09:51:34 +02:00
Mahwash Jamy
49487593e2
Merge branch 'nf-core:dev' into diamond-update 2022-07-28 15:48:59 +02:00