James Fellows Yates
d11257b330
Module update
2022-09-08 08:08:36 +02:00
James A. Fellows Yates
28d8d3f8fb
Merge branch 'dev' into nf-core-template-merge-2.5
2022-08-31 09:16:34 +02:00
nf-core-bot
6dfca81761
Template update for nf-core/tools version 2.5
2022-08-30 13:43:03 +00:00
James Fellows Yates
873a13e028
Merge remote-tracking branch 'origin/dev' into porechop-log
2022-07-29 09:51:34 +02:00
Mahwash Jamy
49487593e2
Merge branch 'nf-core:dev' into diamond-update
2022-07-28 15:48:59 +02:00
sofstam
cecbb41f88
Update centrifuge/kreport
2022-07-27 14:42:35 +02:00
James A. Fellows Yates
64f01fcfe0
Merge branch 'dev' into porechop-log
2022-07-20 14:05:23 +02:00
James Fellows Yates
33a5402b25
Add emitting porechop logs to multiqc and fix collection of others
2022-07-19 13:50:39 +02:00
sofstam
3f5fa8cc7a
Merge branch 'dev' into update_filtlong
2022-07-19 13:50:28 +02:00
mjamy
035b4b7a17
Update the dev branch with the DIAMOND module update
2022-07-15 16:28:07 +02:00
James A. Fellows Yates
c215ed5607
Merge branch 'dev' into motus/merge
2022-07-15 10:52:42 +02:00
sofstam
6b00360ff5
Merge branch 'dev' into update_filtlong
2022-07-15 10:05:43 +02:00
James Fellows Yates
eaa69b65d8
Update mOTUs profile module and mix log for multiqc
2022-07-13 12:38:30 +02:00
sofstam
4a316df209
Update the dev branch with the filtlong update
2022-07-12 17:15:36 +02:00
James Fellows Yates
a0ee82bf43
Add motus/merge and biom support
2022-07-12 11:39:26 +02:00
James A. Fellows Yates
8082c7d108
Merge pull request #97 from nf-core/malt-to-krona
...
Add Krona support for MALT
2022-07-05 15:17:52 +02:00
James A. Fellows Yates
26e31c782d
Merge branch 'dev' into motus
2022-07-04 13:14:42 +02:00
James Fellows Yates
447b8f0905
Get fixed Krona module and add Krona taxonomy to test profile
2022-07-01 17:21:19 +02:00
James Fellows Yates
02c06b9f7b
Add support for MALT display in Krona, tweaks other krona modules to dispaly tool name in output file
2022-06-30 18:33:11 +02:00
James A. Fellows Yates
913080a5b1
Merge pull request #96 from MillironX/feature/kaiju2krona
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Add Krona output for Kaiju profiles
2022-06-29 09:27:25 +02:00
James A. Fellows Yates
5e554a3a0b
Merge pull request #91 from MillironX/feature/kreport2krona
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Add Krona output for Kraken classification
2022-06-27 16:55:55 +02:00
5b80c7cab9
Install KAIJU_KAIJU2KRONA
2022-06-27 08:58:28 -05:00
James Fellows Yates
4ff2145e44
Roll back MALT version
2022-06-20 08:23:14 +02:00
5da8d5b741
Install KRONA_KTIMPORTTEXT
2022-06-14 10:34:34 -05:00
87678c127b
Add KRONA_CLEANUP process module
2022-06-14 10:34:33 -05:00
a84f693479
Install KRAKENTOOLS_KREPORT2KRONA module
2022-06-14 08:13:36 -05:00
JIANHONG OU
c8a59adbce
remove the database auto-download for mOTUs.
2022-06-03 14:13:58 -04:00
James A. Fellows Yates
96fecb2bfc
Merge branch 'dev' into support-aligned-reads
2022-06-03 13:48:54 +02:00
James A. Fellows Yates
53c4399052
Merge branch 'dev' into motus
2022-06-02 21:38:35 +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
JIANHONG OU
68d0cc00fa
add motus profile.
2022-05-23 08:05:06 -04:00
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
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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