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Author SHA1 Message Date
James Fellows Yates
3fa2181f49 Fix prinseq tool selection 2022-05-07 06:15:15 +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
James A. Fellows Yates
e7b54801ed
Merge pull request #75 from nf-core/improve-error-message 
Only create profiler input channels when profiler activated
 2022-05-06 11:51:33 +02:00
Lauri Mesilaakso
e52a40cc9d
Merge pull request #77 from genomic-medicine-sweden/add_nanopore_host_reads_removal_with_minimap2 
Add nanopore host reads removal with minimap2
 2022-05-06 12:29:17 +03:00
Lauri Mesilaakso
02517733aa
Update docs/usage.md 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 10:40:59 +02:00
Lauri Mesilaakso
b0faeedc60
Update workflows/taxprofiler.nf 
Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
 2022-05-06 08:20:31 +02:00
ljmesi
e3e55f57c2 Fix alignment 
Just made this change to see if the CI tests would fail again or if the
failure was just a one of thing.
 2022-05-05 14:02:24 +02:00
ljmesi
6618e8cac6 Change param to a more generic name 2022-05-05 13:20:34 +02:00
ljmesi
557d31dfd2 Add parameter for turning on longread host removal 2022-05-05 13:19:10 +02:00
ljmesi
d94534e8ac Simplify params which control host removal publish 2022-05-05 09:07:33 +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
f4abbe280a Fix back to nf-core modules version 2022-05-03 12:56:49 +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
17039ebc6b Fix type to boolean for flags 2022-05-03 11:07:23 +02:00
ljmesi
4b2a3789cd Update default values for host removal parameters 2022-05-03 11:03:48 +02:00
ljmesi
fa1c132635 Update nextflow_schema 2022-05-03 11:03:25 +02:00
ljmesi
afdebaf09a Remove own modification to a module 2022-05-03 10:15:11 +02:00
ljmesi
5e6be52fab Implement hostremoval 2022-05-03 09:34:27 +02:00
ljmesi
a821f748ee Add modules 2022-05-03 09:28:46 +02:00
James Fellows Yates
d5049a34e4 Add missing close bracket 2022-05-01 07:28:29 +02:00
James Fellows Yates
4094706421 Only create profiler input channels when profiler activate 2022-05-01 07:24:58 +02:00
James Fellows Yates
031cb45934 Add initial longread QC filtering - requires filtlong module update 2022-05-01 07:18:14 +02:00
James A. Fellows Yates
2bae9d58ee
Merge pull request #72 from nf-core/diamond 
Add DIAMOND
 2022-04-30 20:28:28 +02:00
James Fellows Yates
0630fce3b5 Tweak based on official DIAMOND test-data 2022-04-30 08:11:40 +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
120f86e5c7
Merge pull request #67 from genomic-medicine-sweden/classification_kaiju2table 
Add kaiju2table to taxprofiler
 2022-04-26 16:11:47 +02:00
Sofia Stamouli
194b89e66a Prettier 2022-04-26 12:53:39 +02:00
Sofia Stamouli
7afda265c5 Enumerating taxon 2022-04-26 11:27:18 +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
James A. Fellows Yates
bc84afe80d
Merge pull request #66 from nf-core/versions-fix 
Fix version reporting
 2022-04-25 16:38:28 +02:00
Sofia Stamouli
1c694145d4
Merge pull request #65 from genomic-medicine-sweden/classification_kreport 
Add centrifuge kreport in taxprofiler
 2022-04-25 10:14:43 +02:00
Sofia Stamouli
e3a613de00 Prettier 2022-04-25 09:32:25 +02:00
Sofia Stamouli
d8a5c793e2 Remove parameter from nextflow_schema 2022-04-25 09:29:43 +02:00
Sofia Stamouli
ba2479b95b Prettier 2022-04-25 09:26:49 +02:00
Sofia Stamouli
e7e24c2d95 Prettier and suggestions from review 2022-04-25 09:21:29 +02:00
James Fellows Yates
06b38f3699 Fix crash, add missing versions 2022-04-23 08:36:01 +02:00
James Fellows Yates
cda1274918 Moves ordering of modules/subworkflow versions mixing to before custom_dumpsoftwareversions mix, otherwise not used in collectFile 2022-04-23 06:47:59 +02:00
sofstam
c00ca1c2b8 Add centrifuge kreport in taxprofiler 2022-04-22 15:24:10 +02:00
James A. Fellows Yates
63230c3254
Merge pull request #63 from nf-core/maxforks 
Update test.config to only allow maxFork to 1 for MALT_RUN
 2022-04-21 12:57:37 +02:00
James A. Fellows Yates
47a34d4c7e
Merge pull request #59 from nf-core/hostremoval-publish-fix 
Add finer control over for hostremoval saving
 2022-04-21 12:57:09 +02:00
James A. Fellows Yates
cd3c8f6a89
Merge branch 'dev' into hostremoval-publish-fix 2022-04-21 11:43:06 +02:00
James A. Fellows Yates
d850333e11
Linting 2022-04-20 13:42:26 +02:00
James A. Fellows Yates
d031322c16
Update test.config 2022-04-20 13:41:01 +02:00
Sofia Stamouli
e71e7b86a2
Merge pull request #53 from genomic-medicine-sweden/classification_kaiju 
Add kaiju/kaiju in taxprofiler
 2022-04-20 10:57:00 +02:00