millironx/taxprofiler
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582 commits 7 branches 0 tags 7.5 MiB
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207 commits

Author SHA1 Message Date
James Fellows Yates
06659af777 Remove flatten 2022-11-22 13:36:40 +01:00
James Fellows Yates
ebfc84e235 Does the grouping work if we have meta? 2022-11-22 13:26:54 +01:00
James Fellows Yates
21759807f7 Does flatten work? 2022-11-22 12:48:54 +01:00
James Fellows Yates
3102e40052 dump teh db 2022-11-22 12:46:26 +01:00
James Fellows Yates
557f2a4d96 Extra dump 2022-11-22 12:26:46 +01:00
James Fellows Yates
5caebcc6ab Append to correct db 2022-11-22 12:21:59 +01:00
James Fellows Yates
52fc00802b Correct meta name for db meta 2022-11-22 12:19:56 +01:00
James Fellows Yates
b8937748d3 Fix meta.id isssue 2022-11-22 12:18:52 +01:00
James Fellows Yates
db334c5185 Fix missing info 2022-11-22 12:17:08 +01:00
James Fellows Yates
0f298dca43 group krakenuniq reads by pairs or single end 2022-11-22 12:13:08 +01:00
James Fellows Yates
461482d22a Try again wit hthe corret param 2022-11-03 15:02:22 +01:00
James Fellows Yates
93f38b14a8 Save report 2022-11-03 15:01:00 +01:00
James Fellows Yates
21a76c2449 Fix cardinality issue 2022-11-03 14:56:26 +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
f1778acf35
Apply review suggestion 2022-10-31 09:31:13 +01:00
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
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
Mahwash Jamy
86ca71cfd4 include krakenuniq in profiling subworkflow 2022-10-25 09:45:05 +00:00
Sofia Stamouli
8c3e80b6ea Add helptest to nextflow_schema,add versions to longread_preprocessing 2022-10-25 11:13:26 +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
385507ec6f refactor: use tool name 'bracken' only 2022-10-21 10:03:36 +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
Sofia Stamouli
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +02:00
Moritz E. Beber
48b00b7d62 refactor: create standardized Bracken reports 2022-10-17 17:33:24 +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
Moritz E. Beber
ca38d002de feat: integrate Bracken into the profiling pipeline 2022-10-14 12:18:07 +02:00
James Fellows Yates
56bae85755 Remove necessity of patch 2022-10-11 12:38:18 +02:00
Moritz E. Beber
180cac0395 fix: adapt to new samtools/view input 2022-10-05 13:49:35 +02:00
Moritz E. Beber
f5af9fd939 fix: adjust import paths to re-organization 2022-10-05 13:40:43 +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
87edc4569c Move to a function 2022-09-27 15:46:17 +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
1584d6fc51 Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-09-19 10:43:04 -04:00
James A. Fellows Yates
016efcb807
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-16 16:02:38 +02:00
James A. Fellows Yates
f43c54317c
Update subworkflows/local/standardisation_profiles.nf 
Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com>
 2022-09-16 15:20:47 +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
Rafal Stepien
768f9980d8 Add pep_input_base_dir to workflow. Just need to update modules 2022-09-15 12:31:49 -04:00
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
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 A. Fellows Yates
cc5df924e4
Merge branch 'dev' into module-update 2022-09-08 13:36:21 +02:00