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 |
|