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1006 commits 7 branches 0 tags 7.5 MiB
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179 commits

Author SHA1 Message Date
sofstam
e5bb627402 Apply review suggestions 2022-12-01 11:12:31 +01:00
James A. Fellows Yates
4f6eb6fd75
Merge pull request #153 from mjamy/add-krakenuniq-module 
Add krakenuniq module
 2022-12-01 09:03:29 +01:00
sofstam
933b820c19 Apply review suggestions 2022-11-29 16:57:07 +01:00
Sofia Stamouli
7e3ece53bd
Update modules.config 2022-11-29 13:31:00 +01:00
Sofia Stamouli
0088b07220
Fix trailing whitespace 2022-11-29 13:28:04 +01:00
James A. Fellows Yates
770a35d7ac
Update conf/modules.config 2022-11-29 12:49:20 +01:00
Sofia Stamouli
ba727a81ae Fix left-padding spaces 2022-11-29 12:45:14 +01:00
Sofia Stamouli
71b52b9c94 Apply review suggestions 2022-11-29 11:58:23 +01:00
sofstam
49af33f68e Include NCBI_id, read counts and mgc arguments in motus 2022-11-29 11:07:29 +01:00
James Fellows Yates
9feb6c2db6 Update MALT 2022-11-24 14:44:04 +01:00
Sofia Stamouli
d2195e9eda
Merge branch 'dev' into short_reads_samtools 2022-11-04 11:47:36 +01:00
Sofia Stamouli
b5e6639f9d
Apply review suggestions 2022-11-03 14:12:05 +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
e4307ad8ab Change modules.config to include porechop_porechop 2022-11-01 20:50:42 +01:00
Mahwash Jamy
febcbfc057 add missing parameters to nextflow.config 2022-10-31 16:07:53 +00:00
Mahwash Jamy
3147a80a56 Merge branch 'dev' of https://github.com/mjamy/taxprofiler into add-krakenuniq-module 2022-10-31 15:36:57 +00:00
Sofia Stamouli
0e0c55d3b0
Update modules.config 2022-10-31 12:35:51 +01:00
Sofia Stamouli
a4b5fa9f57
Fix trailing space 2022-10-31 12:17:49 +01:00
Sofia Stamouli
1d1047374b
Fix EditorConfig format 2022-10-31 12:09:25 +01:00
Sofia Stamouli
c4a7d094c8 Fix EditorConfig check 2022-10-28 14:33:44 +02:00
Sofia Stamouli
5b99d9024a Add samtools stats for short-reads 2022-10-28 14:24:33 +02:00
Sofia Stamouli
f87131c7b1 Save samtools stats output 2022-10-28 14:10:24 +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
76a662ecc5 Fix adapterremoval adapter conflict and add optional adapter list file 2022-10-27 12:17:19 +00:00
Mahwash Jamy
f4717be9ab add krakenuniq to modules.config 2022-10-25 09:50:44 +00:00
Moritz E. Beber
c7c7a7f678 refactor: change Bracken prefix to be more specific 2022-10-19 16:20:09 +02:00
Sofia Stamouli
7881ba9aef Fix the amount of left-padding spaces 2022-10-18 17:50:49 +02:00
Sofia Stamouli
8eddb32b88 Add Falco as an alternative to FastQC 2022-10-18 17:43:16 +02:00
Moritz E. Beber
ca38d002de feat: integrate Bracken into the profiling pipeline 2022-10-14 12:18:07 +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
43a8aa4405 Remove detect_reads.py and replace remaining checks with nextflow code instead 2022-09-27 15:32:51 +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
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
19a195ed14 Append profiler to resulting file 2022-09-15 12:30:39 +02:00
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 Fellows Yates
832d981976 Don't have per sample directory as unnecessary if file names are unique with the db in them 2022-09-07 12:22:17 +02:00
James Fellows Yates
7c5f9d0c24 Start work on more merging tools 2022-09-06 17:34:45 +02:00
James A. Fellows Yates
13e9957e14 Fixes process selector warning 2022-09-02 06:03:05 +00:00
James Fellows Yates
2cc07183a0 Standardise QC parameter system and turn on both porechop/filtlong in tests 2022-08-30 13:58:58 +02:00
James Fellows Yates
a97bb69cd2 Prettier 2022-08-23 14:24:57 +02:00
James A. Fellows Yates
de70b0a01d
Merge pull request #109 from nf-core/centrifuge_mqc 
Trying to get Centrifuge output into MQC
 2022-07-29 13:36:25 +02:00
mjamy
5cdf5e958a Updated modules.config to add 'log' in diamond config 2022-07-28 16:08:15 +02:00
sofstam
71cf32cc6a Add error strategy for centrifuge/kreport 2022-07-28 08:54:32 +02:00
James A. Fellows Yates
65ae82efc4 Define separte krakena nd centrigfue modules 2022-07-26 18:37:33 +00:00
James A. Fellows Yates
e76b299705 Start working getting kraken and centrifuge working in MQC 2022-07-26 08:18:54 +00:00
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
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
Thomas A. Christensen II
069370db86
Add unclassified and verbose flags to kaiju2krona 2022-06-28 09:00:42 -05:00
Thomas A. Christensen II
0e8edd5b2f
Add output configuration for Kraken Krona chart 2022-06-27 08:25:47 -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 A. Fellows Yates
c9581b1796
Merge branch 'dev' into support-aligned-reads 2022-06-02 12:45:29 +02:00
James Fellows Yates
d3d28da1b1 Update after review 2022-06-02 11:53:53 +02:00
James Fellows Yates
16ec5bf74a Update parameter names 2022-05-31 20:11:19 +02:00
JIANHONG OU
f0eb88cbe2 add mOTUs to modules.config 2022-05-31 08:57:00 -04:00
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 A. Fellows Yates
d67543503b
Apply suggestions from code review 
Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
 2022-05-07 13:15:21 +02:00
James Fellows Yates
0f651873dd Linting 2022-05-07 06:12:24 +02:00
James Fellows Yates
47a5ae0cff Add FASTP complexity option 2022-05-07 06:09:05 +02:00
James Fellows Yates
87a1d80519 Add working output for Kraken2/Centrifuge/DIAMOND 2022-05-07 05:22:35 +02:00
ljmesi
d94534e8ac Simplify params which control host removal publish 2022-05-05 09:07:33 +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
sofstam
d082d67bcb Add kaiju2table to taxprofiler 2022-04-25 17:36:29 +02:00
Sofia Stamouli
e7e24c2d95 Prettier and suggestions from review 2022-04-25 09:21:29 +02:00
sofstam
c00ca1c2b8 Add centrifuge kreport in taxprofiler 2022-04-22 15:24:10 +02:00
James A. Fellows Yates
cd3c8f6a89
Merge branch 'dev' into hostremoval-publish-fix 2022-04-21 11:43:06 +02:00
Sofia Stamouli
236141f065 Resolve conflicts with dev 2022-04-20 10:17:10 +02:00
James A. Fellows Yates
d16cd75652
Merge branch 'dev' into hostremoval-publish-fix 2022-04-20 09:53:51 +02:00
sofstam
1b7ff2265d Update usage.md, reformat test.config and modules.config 2022-04-19 13:04:58 +02:00
James Fellows Yates
9880baa0b8 Get build directory working 2022-04-18 06:37:23 +02:00
James Fellows Yates
2cfcdf2dd2 Add finer controler over for hostremoval saving 2022-04-17 22:27:04 +02:00
James Fellows Yates
cc73cdd51d Add generation of taxon-table like output for MALT 2022-04-16 07:42:30 +02:00
sofstam
68ce5843a4 Add kaiju in taxprofiler 2022-04-13 18:51:56 +02:00
James A. Fellows Yates
70f94603b0
Merge branch 'dev' into hostremoval 2022-04-13 13:59:51 +02:00
James Fellows Yates
dfeaa0d1fe Rename subworkflow parameters for consistency 2022-04-13 12:00:28 +02:00
James A. Fellows Yates
967b1f7d6e
Merge branch 'dev' into run-merging 2022-04-12 09:28:10 +02:00
James Fellows Yates
a5f4fc42d5 Fix run merging for unmerged PE data 2022-04-12 09:25:27 +02:00
James A. Fellows Yates
025083061e
Merge branch 'dev' into hostremoval 2022-04-11 13:36:03 +02:00
James Fellows Yates
082093f3de Prettier 2022-04-10 06:44:10 +02:00
James Fellows Yates
ecf0eea4f9 Move profiling to subworkflow and standardise outputs 2022-04-10 06:43:30 +02:00
James Fellows Yates
ca011ccc5b Fix cat_fastq naming logic? 2022-04-08 13:28:37 +02:00
James Fellows Yates
d130a72d74 Get this working 2022-04-08 13:09:23 +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
Moritz E. Beber
7ab3aa546b refactor: use flags to publish reads 2022-04-06 10:27:11 +02:00
Moritz E. Beber
018b9a8ea6 refactor: do not generally publish output 2022-04-06 10:21:43 +02:00
Moritz E. Beber
8827b143a2 fix: disable publishing correctly 2022-04-05 20:56:19 +02:00
Moritz E. Beber
af12435fa5 fix: use parameter for publish mode everywhere 2022-04-05 20:56:19 +02:00