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genomic-medicine-sweden
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jasen
Bacterial typing pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
https://jasen.readthedocs.io/en/latest/
GNU General Public License v3.0
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Add more snippy output files
#373
mhkc
opened
5 days ago
0
Makefile using system tabix and bgzip
#372
JPWerling
opened
1 week ago
0
Fix channel of bug
#371
ryanjameskennedy
closed
1 week ago
0
Channel.of creating problems with executing all samples in csv
#370
ryanjameskennedy
closed
1 week ago
0
Fix jasen first bug
#369
ryanjameskennedy
closed
1 week ago
0
Jasen only runs first sample in csv
#368
ryanjameskennedy
closed
1 week ago
0
Update prp to v0.11.1
#367
ryanjameskennedy
closed
1 week ago
0
Add tb grading rules bed
#366
ryanjameskennedy
closed
2 weeks ago
0
Cleanup config files and duplicated code
#365
ryanjameskennedy
opened
2 weeks ago
0
Add read downsampling as a pre processing step
#364
mhkc
closed
2 weeks ago
0
Add FoHM mutations to TBProfiler
#363
ryanjameskennedy
opened
3 weeks ago
0
Add down sampling of reads as a pre-processing step
#362
mhkc
closed
3 weeks ago
1
Add human read depletion as optional pre-processing step
#361
mhkc
opened
3 weeks ago
0
Rm copy_to_cron module
#360
ryanjameskennedy
closed
3 weeks ago
0
Update cron copy using config
#359
ryanjameskennedy
closed
3 weeks ago
0
Fixes to hopper config and saureus workflow
#358
ryanjameskennedy
closed
4 weeks ago
0
Jasen hopper config and saureus workflow fixes
#357
ryanjameskennedy
closed
4 weeks ago
0
Add postal code entry to "sample_list" file and provide in output
#356
hrydbeck
opened
1 month ago
0
Create subrun command to partially run jasen modules
#355
ryanjameskennedy
opened
1 month ago
0
Two unnecessary processes for spades module
#354
ryanjameskennedy
closed
1 month ago
1
TB workflow runs post_align_qc twice
#353
ryanjameskennedy
opened
2 months ago
0
Add streptococcus workflow
#352
ryanjameskennedy
closed
4 weeks ago
0
Makefile species-specific installation
#351
ryanjameskennedy
opened
2 months ago
1
Add ska to base
#350
ryanjameskennedy
closed
1 month ago
0
Mask out IS6110 from delly variants
#349
mhkc
opened
2 months ago
0
Add resistance determining regions to tb expert rules bed file as IGV track
#348
ryanjameskennedy
closed
2 weeks ago
0
Update tbdb submodule
#347
ryanjameskennedy
closed
2 months ago
0
Update tbdb submodule
#346
ryanjameskennedy
closed
2 months ago
0
Error for "Creating WHO FoHM TBDB ..." when running make install
#345
hrydbeck
closed
2 months ago
0
299 add qc for nanopore data
#344
Emkago
opened
2 months ago
2
Update to v0.9.0
#343
ryanjameskennedy
closed
2 months ago
0
Update to v0.9.0
#342
ryanjameskennedy
closed
2 months ago
0
Download medaka models
#341
Emkago
opened
3 months ago
0
Add split kmer analysis tool to JASEN
#340
ryanjameskennedy
closed
1 month ago
0
Add pHierCC module for Enterobase related actions
#339
ryanjameskennedy
opened
3 months ago
0
Updated JASEN to support PRP v0.10.0
#338
mhkc
closed
2 months ago
1
297 add nanopore test data
#337
Emkago
closed
3 months ago
0
Update tbprofiler to version 6.3
#336
mhkc
closed
3 months ago
0
Update TbProfiler to version 6.3
#335
mhkc
closed
3 months ago
0
Changes to TbProfiler changed their output format with version 6
#334
mhkc
closed
2 months ago
1
332 fix cdm input bug
#333
ryanjameskennedy
closed
3 months ago
0
.cdmpy output needs full filepath for qc_result.json file
#332
ryanjameskennedy
closed
3 months ago
0
V0.8.0
#331
svartapaerlan
closed
4 months ago
0
Fix tb workflow bug
#330
ryanjameskennedy
closed
4 months ago
0
Poor performance of Serotypefinder using fastq files as input
#329
mhkc
opened
4 months ago
0
Add profile for Borrelia
#328
ryanjameskennedy
opened
5 months ago
0
Additional requirements
#327
hrydbeck
opened
5 months ago
0
Makefile core usage argument
#326
sylvinite
opened
5 months ago
0
324 improve the pipeline description
#325
mhkc
closed
5 months ago
0
Improve the pipeline description
#324
mhkc
closed
5 months ago
0
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