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228 commits

Author SHA1 Message Date
James Fellows Yates
0dccfddc24 Switch order back 2022-12-03 21:38:25 +01:00
James A. Fellows Yates
cf8ad96771
Update subworkflows/local/profiling.nf 2022-12-02 15:09:08 +01:00
James Fellows Yates
ab42f6b662 wteak message 2022-12-02 12:49:00 +01:00
James Fellows Yates
a3cd188b1f Merge branch 'sep-krakenuniq-test' of github.com:nf-core/taxprofiler into sep-krakenuniq-test 2022-12-02 12:48:18 +01:00
James Fellows Yates
de74e4f727 Fix centrifuge warning, filter out long reads from Brakcen, add some caveat docs to usage.md 2022-12-02 12:47:14 +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 A. Fellows Yates
4f6eb6fd75
Merge pull request #153 from mjamy/add-krakenuniq-module
Add krakenuniq module
2022-12-01 09:03:29 +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
Moritz E. Beber
ddcf38de22 refactor: make mappings explicit 2022-11-29 10:14:20 +01:00
James Fellows Yates
9feb6c2db6 Update MALT 2022-11-24 14:44:04 +01:00
sofstam
481f90589c Apply review suggestions 2022-11-23 09:08:22 +01:00
sofstam
30af26a8b3 Include the mapped reads in samtools stats 2022-11-22 16:50:50 +01:00
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
Sofia Stamouli
d2195e9eda
Merge branch 'dev' into short_reads_samtools 2022-11-04 11:47:36 +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
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
ce611d6efd Add bowtie2 mapped reads 2022-10-31 10:04:51 +01:00
Sofia Stamouli
f1778acf35
Apply review suggestion 2022-10-31 09:31:13 +01:00
Sofia Stamouli
5b99d9024a Add samtools stats for short-reads 2022-10-28 14:24:33 +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
08d61065e5 Add adapterlist to AR2 subworkflow 2022-10-27 12:23:27 +00:00
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
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