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moka-guys
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automate_demultiplex
Scripts for routine analysis of clinical next generation sequencing (NGS) data at Synnovis Genetics
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Feature/tsosplitting
#507
rebeccahaines1
closed
1 year ago
0
automate exome depth
#506
aledj2
closed
1 year ago
1
replace Viapath with GSTT (future proof incase KCL can also use these scripts)
#505
aledj2
closed
5 months ago
1
Can we add Pan5180 as a dummy/development Pan number so it doesn't error but also doesn't process past demultiplexing
#504
aledj2
closed
1 year ago
0
add HRD and OKD to list of allowed prefixes (maybe more?)
#503
aledj2
closed
5 months ago
1
Having None here results in stderr when executing dx run commands. Can this be changed to something else?
#502
aledj2
closed
5 months ago
1
v44.7.0
#501
RachelDuffin
closed
1 year ago
0
V44.7.0
#500
RachelDuffin
closed
1 year ago
0
correct username
#499
aledj2
closed
1 year ago
0
new TSO BEDfile Pan5130
#498
rebeccahaines1
closed
1 year ago
0
logfile list might be empty, eg if copy of failed integrity check
#497
aledj2
closed
5 months ago
1
coverage results should be in subfolders by Pan number
#496
rebeccahaines1
closed
1 year ago
0
Update incorrect RPKM VCP3 pan number
#495
RachelDuffin
closed
1 year ago
0
Add pannumber assignment command for coverage subfolder
#494
RachelDuffin
closed
1 year ago
0
Prostate panel r430
#493
rebeccahaines1
closed
1 year ago
0
v44.6.0
#492
RachelDuffin
closed
1 year ago
0
change hours to 12
#491
aledj2
closed
1 year ago
1
Feature/fix duty csv
#490
RachelDuffin
closed
1 year ago
0
Merge master into develop
#489
RachelDuffin
closed
1 year ago
0
update instance type
#488
aledj2
closed
1 year ago
1
exclude neg control from the TSO500 depends on list
#487
aledj2
closed
1 year ago
1
Update variable name
#486
RachelDuffin
closed
1 year ago
0
Update TSO and ADX pipeline IDs, add comments to guide on updating pa…
#485
RachelDuffin
closed
1 year ago
0
Feature/duty csv
#484
RachelDuffin
closed
1 year ago
0
Move cluster density calculation to demultiplex.py
#483
RachelDuffin
closed
1 year ago
1
Remove MokaCAN as obsolete
#482
RachelDuffin
closed
1 year ago
0
Change upload_agent_script_logfiles directory to match name of logfiles stored within it
#481
RachelDuffin
closed
5 months ago
2
Move email template string to an actual template in a templates directory
#480
RachelDuffin
closed
5 months ago
2
Refactor upload and setoff workflows script and add test suite
#479
RachelDuffin
closed
5 months ago
2
Develop - v44.4.0
#478
RachelDuffin
closed
1 year ago
0
Dry lab pan numbers and TSO and multiqc app updates
#477
rebeccahaines1
closed
1 year ago
0
Feature/mokapipe v2.18
#476
RachelDuffin
closed
1 year ago
0
Merge main into develop
#475
RachelDuffin
closed
1 year ago
0
Create a github actions page that can be accessed by both the team / other teams
#474
RachelDuffin
opened
1 year ago
0
Use larger instance for SNP multiqc
#473
RachelDuffin
closed
1 year ago
2
Update git tag as per code review request
#472
RachelDuffin
closed
5 months ago
1
v44.3.7
#471
natashapinto
closed
1 year ago
0
V44.3.7
#470
natashapinto
closed
1 year ago
0
Move mokapipe_fh_gatk_timeout_args to dxapp json file
#469
RachelDuffin
closed
5 months ago
1
change None to BSPS_MD
#468
aledj2
closed
1 year ago
1
V44.3.7
#467
natashapinto
closed
1 year ago
0
Tsodrylab
#466
natashapinto
closed
1 year ago
0
Remove obsolete pan numbers
#465
RachelDuffin
closed
1 year ago
3
Feature/mokapipe v2.17
#464
RachelDuffin
closed
1 year ago
1
Feature/mokapipe v2.17
#463
RachelDuffin
closed
1 year ago
1
Alter CollectIlluminaLaneMetrics calculation function to only run if the output files are not present in the runfolder
#462
RachelDuffin
closed
5 months ago
3
Add more comprehensive error logging to upload_and_setoff_workflows script
#461
RachelDuffin
closed
5 months ago
2
update multiqc app version to v1.16.0
#460
rebeccahaines1
closed
1 year ago
1
Change all mention of 'Viapath' to 'Synnovis'
#459
RachelDuffin
closed
5 months ago
2
Add congenica upload app version to WES query
#458
RachelDuffin
opened
1 year ago
0
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