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 |
|
Sofia Stamouli
|
d2195e9eda
|
Merge branch 'dev' into short_reads_samtools
|
2022-11-04 11:47:36 +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 |
|
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 |
|
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 |
|
James Fellows Yates
|
d11257b330
|
Module update
|
2022-09-08 08:08:36 +02:00 |
|
James Fellows Yates
|
7c5f9d0c24
|
Start work on more merging tools
|
2022-09-06 17:34:45 +02:00 |
|
James A. Fellows Yates
|
8456f934ed
|
Update subworkflows/local/visualization_krona.nf
|
2022-09-02 16:15:46 +02:00 |
|
James A. Fellows Yates
|
13e9957e14
|
Fixes process selector warning
|
2022-09-02 06:03:05 +00:00 |
|