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Author SHA1 Message Date
James A. Fellows Yates
621b6a3d09
Add comments about MALT id replacement and refactor for simplicity 2022-06-10 11:27:51 +02:00
James Fellows Yates
800c0dd2aa Merge branch 'support-aligned-reads' of github.com:nf-core/taxprofiler into support-aligned-reads 2022-06-09 08:16:01 +02:00
James Fellows Yates
490a8a8a84 Remove dump 2022-06-09 08:15:58 +02:00
James A. Fellows Yates
ebdd5683b2
Apply suggestions from code review 2022-06-03 22:33:48 +02:00
James Fellows Yates
9462032d00 Fix MALT save_alignemnts reads and some clean up 2022-06-03 22:29:04 +02:00
James Fellows Yates
d48b3be5a7 Tweak DIAMOND save_reads message 2022-06-03 13:55:17 +02:00
James Fellows Yates
3313b90453 Fix JSOn schema 2022-06-03 13:50:48 +02:00
James A. Fellows Yates
96fecb2bfc
Merge branch 'dev' into support-aligned-reads 2022-06-03 13:48:54 +02:00
James A. Fellows Yates
43ea8d299c
Merge pull request #74 from nf-core/add-filtlong 
Add initial longread QC filtering - requires filtlong module update
 2022-06-02 20:10:46 +02:00
James Fellows Yates
2838c136bd Prettier 2022-06-02 12:51:39 +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 A. Fellows Yates
a196e0f628
Merge branch 'dev' into add-filtlong 2022-06-02 11:51:26 +02:00
James A. Fellows Yates
dfcaaae1fb
Merge pull request #83 from ZandraFagernas/dev 
Uploaded logo
 2022-06-02 11:31:32 +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
792e2d019b Fix merge error in schema 2022-05-31 13:06:48 +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
James Fellows Yates
77da358e87 Separate dark and light mode logos, add to README and add to MQC report 2022-05-31 12:45:38 +02:00
ZandraFagernas
74b48f0919
Add files via upload 2022-05-28 13:29:24 +02:00
James A. Fellows Yates
ba75685550
Merge pull request #81 from nf-core/nf-core-template-merge-2.4 
Important! Template update for nf-core/tools v2.4
 2022-05-19 11:00:48 +01:00
Moritz E. Beber
a9fbe47992
Merge branch 'dev' into nf-core-template-merge-2.4 2022-05-19 08:42:28 +02:00
nf-core-bot
a560492353 Template update for nf-core/tools version 2.4 2022-05-16 10:22:38 +00:00
James A. Fellows Yates
63d9cbbdfd
Merge pull request #80 from nf-core/activate-pipeline-specific-profiles 
Activate institutional specific profiles
 2022-05-12 11:00:49 +02:00
James A. Fellows Yates
aca7bc439d
Update nextflow.config 2022-05-12 08:08:14 +01:00
James A. Fellows Yates
fd71b71929
Merge pull request #79 from nf-core/fastp-complexity 
Add FASTP complexity option
 2022-05-07 14:05:32 +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
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