millironx/taxprofiler
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1048 commits 7 branches 0 tags 7.5 MiB
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157 commits

Author SHA1 Message Date
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 
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 
Add Krona output for Kraken classification
 2022-06-27 16:55:55 +02:00
Thomas A. Christensen II
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
Thomas A. Christensen II
5da8d5b741
Install KRONA_KTIMPORTTEXT 2022-06-14 10:34:34 -05:00
Thomas A. Christensen II
87678c127b
Add KRONA_CLEANUP process module 2022-06-14 10:34:33 -05:00
Thomas A. Christensen II
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 
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