James A. Fellows Yates
96fecb2bfc
Merge branch 'dev' into support-aligned-reads
2022-06-03 13:48:54 +02:00
James Fellows Yates
16ec5bf74a
Update parameter names
2022-05-31 20:11:19 +02:00
James Fellows Yates
310ac6b450
Merge branch 'dev' of github.com:nf-core/taxprofiler into add-filtlong
2022-05-31 13:05:52 +02:00
James Fellows Yates
87a1d80519
Add working output for Kraken2/Centrifuge/DIAMOND
2022-05-07 05:22:35 +02:00
ljmesi
59c7f5a5b1
Update samtools/bam2fq
2022-05-05 08:38:41 +02:00
ljmesi
f4abbe280a
Fix back to nf-core modules version
2022-05-03 12:56:49 +02:00
ljmesi
58d4dec70b
Update samtools view
2022-05-03 11:09:54 +02:00
ljmesi
afdebaf09a
Remove own modification to a module
2022-05-03 10:15:11 +02:00
ljmesi
a821f748ee
Add modules
2022-05-03 09:28:46 +02:00
James Fellows Yates
031cb45934
Add initial longread QC filtering - requires filtlong module update
2022-05-01 07:18:14 +02:00
James Fellows Yates
8126d16dee
Add draft version of DIAMOND
2022-04-29 21:59:42 +02:00
sofstam
d082d67bcb
Add kaiju2table to taxprofiler
2022-04-25 17:36:29 +02:00
sofstam
c00ca1c2b8
Add centrifuge kreport in taxprofiler
2022-04-22 15:24:10 +02:00
Sofia Stamouli
236141f065
Resolve conflicts with dev
2022-04-20 10:17:10 +02:00
James A. Fellows Yates
6fecb3eeb7
Merge pull request #54 from nf-core/dev
...
Get upstream changes
2022-04-16 06:17:33 +02:00
sofstam
68ce5843a4
Add kaiju in taxprofiler
2022-04-13 18:51:56 +02:00
James Fellows Yates
de57340526
Start work
2022-04-13 11:49:35 +02:00
James A. Fellows Yates
025083061e
Merge branch 'dev' into hostremoval
2022-04-11 13:36:03 +02:00
Sofia Stamouli
fd5ebea9a6
Remove old centrifuge module
2022-04-08 10:57:58 +02:00
sofstam
606e5da7d5
Check if PR works with centrifuge/centrifuge module
2022-04-07 16:13:17 +02:00
James A. Fellows Yates
b554aa3e4d
Merge branch 'dev' into hostremoval
2022-04-07 14:00:10 +02:00
James A. Fellows Yates
23fb319779
Merge branch 'dev' into complexity-filter-bbduk
2022-04-05 13:11:15 +02:00
Moritz E. Beber
c54c32c494
chore: update adapterremoval
2022-04-05 10:18:34 +02:00
James A. Fellows Yates
3d662d2e06
Merge branch 'dev' into complexity-filter-bbduk
2022-04-04 21:19:36 +02:00
James Fellows Yates
a384162810
Add prinseq as alternative complexity filtering
2022-04-04 21:16:51 +02:00
sofstam
d897c922b2
Add centrifuge classificatioN
2022-04-04 13:51:51 +02:00
James A. Fellows Yates
b2e29ea23a
Merge branch 'dev' into hostremoval
2022-04-03 17:24:07 +02:00
James Fellows Yates
066ceb2bca
Remove flagstat as bowtie2 reports this itself
2022-04-03 17:23:14 +02:00
James Fellows Yates
482112bb42
Start work on host removal
2022-04-03 07:58:40 +02:00
Moritz E. Beber
be93eae640
fix: insert .fastq
file extension
...
The MetaPhlAn3 module computes the input type from the file extension
without the possibility to configure an override. Since AdapterRemoval2
creates files without `.fastq` extensions, MetaPhlAn3 input was determined
to be SAM.
2022-04-02 21:50:13 +02:00
James Fellows Yates
b055df5ea0
Add bbduk complexity (entropy-based) filtering
2022-04-02 17:02:05 +02:00
Moritz E. Beber
4d2960c06f
chore: add metaphlan3 module
2022-04-02 14:59:44 +02:00
James Fellows Yates
c4c93bd59d
Start working on adding adapterremoval
2022-03-31 15:31:45 +02:00
sofstam
37a70dc3e3
Merge branch 'dev' into classification_centrifuge
2022-03-25 16:18:35 +01:00
James A. Fellows Yates
edce6603ef
Merge branch 'dev' into nf-core-template-merge-2.3.2
2022-03-24 14:10:58 +01:00
sofstam
3ff54e620e
Add centrifuge classification
2022-03-24 13:02:25 +01:00
nf-core-bot
6b939e6728
Template update for nf-core/tools version 2.3.1
2022-03-23 13:57:56 +00:00
James A. Fellows Yates
3079f16861
Merge branch 'dev' into database-untar
2022-03-21 19:55:36 +01:00
James A. Fellows Yates
631c115e10
Adds PoC of untarring system
2022-03-21 14:58:19 +00:00
James Fellows Yates
c7f022008c
Start getting database prep ready
2022-03-21 15:07:59 +01:00
ljmesi
16be676d72
Add Porechop module
2022-03-18 14:34:10 +01:00
James Fellows Yates
e39c6a8ccb
Fix MALT multiqc report clash
2022-03-03 18:04:03 +01:00
James Fellows Yates
2c183ed2ed
Add Kraken2 and MALT/run as Proof of Concept (currnetly MQC issue)
2022-03-03 17:42:02 +01:00
James Fellows Yates
278f5605ca
Added database preparation and final channel for profiling
2022-02-19 12:36:08 +01:00
James Fellows Yates
cf55cc592c
Get skeleton read processing to input for profiling
2022-02-18 16:51:01 +01:00
James Fellows Yates
12e7b428f2
initial template build from nf-core/tools, version 2.2
2022-02-18 07:55:14 +01:00