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1046 commits 7 branches 0 tags 7.5 MiB
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158 commits

Author SHA1 Message Date
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
Rafal Stepien
9349346864 Remove --pep parameter and leave just --input 2022-09-16 10:14:01 -04:00
James A. Fellows Yates
016efcb807
Merge branch 'dev' into metaphlan3/mergemetaphlantables 2022-09-16 16:02:38 +02:00
James Fellows Yates
63b3cc678f Merge branch 'motus-merge-meta' of github.com:nf-core/taxprofiler into motus-merge-meta 2022-09-16 10:25:28 +02:00
James Fellows Yates
c5cc21d29e Update motus merge module to remove unused channel 2022-09-16 10:25:24 +02:00
James A. Fellows Yates
2c83b367a7
Apply suggestions from code review 2022-09-16 09:28:42 +02:00
James Fellows Yates
4e7857e2ed Standardise mOTUs table merge 2022-09-16 08:36:34 +02:00
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 A. Fellows Yates
5414ae2e55
Apply suggestions from code review 2022-09-14 11:20:40 +02:00
James Fellows Yates
abbbf9c7ab Update to use tar module compatible for our test databases 2022-09-14 11:16:28 +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
b28052f1ec
Remove patch from modules.json 2022-09-09 11:15:25 +02:00
James Fellows Yates
f087136ec9 use proper working FASTP module 2022-09-09 11:12:47 +02:00
James Fellows Yates
60224e9149 Patch fastp until I have an OK on the module update 2022-09-08 14:25:23 +02:00
James Fellows Yates
fc26948950 Fix MultiQC 2022-09-08 12:49:38 +02:00
James Fellows Yates
d11257b330 Module update 2022-09-08 08:08:36 +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
9bc45a3f24 Update centrifuge/kreport 2022-07-27 14:44:26 +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 Fellows Yates
d83c747533 Fix modules JSON 2022-07-15 12:38:20 +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
1fbe241d27 Update filtlong module 2022-07-12 17:43:52 +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 
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
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
2838c136bd Prettier 2022-06-02 12:51:39 +02:00
James Fellows Yates
fa70a413cb Use finally working filtlong module 2022-05-31 21:12:09 +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
f14141574e fix the end line issue for modules.json 2022-05-25 08:03:23 -04:00
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
5b7b214156 Fix formatting with prettier 2022-05-05 08:40:53 +02:00
ljmesi
59c7f5a5b1 Update samtools/bam2fq 2022-05-05 08:38:41 +02:00
ljmesi
c833d4fd9a Fix issues found with prettier 2022-05-03 11:42:05 +02:00
ljmesi
58d4dec70b Update samtools view 2022-05-03 11:09:54 +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
a4a9b161d8 Lintin 2022-04-29 22:02:44 +02:00
James Fellows Yates
8126d16dee Add draft version of DIAMOND 2022-04-29 21:59:42 +02:00
Sofia Stamouli
f4480feb9b Prettier 2022-04-25 17:45:26 +02:00
sofstam
d082d67bcb Add kaiju2table to taxprofiler 2022-04-25 17:36:29 +02:00
Sofia Stamouli
ba2479b95b Prettier 2022-04-25 09:26:49 +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 Fellows Yates
d0256ec937 Prettier 2022-04-16 07:45:24 +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
6736a2a980 Update README.md, nextflow_schema.json 2022-04-13 19:00:52 +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
63bc597daf Prettier 2022-04-08 11:01:45 +02:00
Sofia Stamouli
fd5ebea9a6 Remove old centrifuge module 2022-04-08 10:57:58 +02:00
Sofia Stamouli
3d45ac57ae Prettier 2022-04-07 16:42:22 +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
59b2088aa1 style: apply prettier 2022-04-05 11:16:43 +02:00
Moritz E. Beber
c54c32c494 chore: update adapterremoval 2022-04-05 10:18:34 +02:00
James Fellows Yates
bb6dd738bd Merge branch 'complexity-filter-bbduk' of github.com:nf-core/taxprofiler into complexity-filter-bbduk 2022-04-04 21:21:34 +02:00
James Fellows Yates
613f6a5565 Prettier 2022-04-04 21:21:29 +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 Fellows Yates
a76576c16b Prettier 2022-04-03 17:24:50 +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
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
b04cfec2c2 Prettier linting 2022-04-01 11:13:36 +02:00
James Fellows Yates
c4c93bd59d Start working on adding adapterremoval 2022-03-31 15:31:45 +02:00
James Fellows Yates
eada201eb2 Prettier 2022-03-28 16:47:37 +02:00
James Fellows Yates
98dc8014a5 Fix kraken2 module 2022-03-28 16:46:45 +02:00
sofstam
16bdc79cc0 Apply prettier 2022-03-25 16:30:26 +01:00
sofstam
37a70dc3e3 Merge branch 'dev' into classification_centrifuge 2022-03-25 16:18:35 +01:00
James Fellows Yates
494c641fb8 Prettier 2022-03-24 15:37:42 +01:00
James Fellows Yates
e3be393f16 Fix broken json 2022-03-24 14:18:15 +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