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AfshinLab
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BLR
MIT License
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Fix CI linting with flake8
#84
pontushojer
closed
3 days ago
0
Load R before submitting SLURM batch job (and other necessary modules)
#83
ajdesalvio
opened
3 days ago
1
Unterminated f-string in extract_barcodes.py
#82
ajdesalvio
closed
3 days ago
2
Improve documentation
#81
pontushojer
opened
11 months ago
0
Update anew
#80
pontushojer
closed
11 months ago
0
Detect sample sex from input
#79
pontushojer
opened
11 months ago
0
Automatically filter out barcodes with too many molecules
#78
pontushojer
opened
12 months ago
0
Add Haplotagging support
#77
pontushojer
opened
12 months ago
0
Re-call SNVs after phasing
#76
pontushojer
opened
12 months ago
0
Make use of molecule information in LinkFragments
#75
pontushojer
opened
12 months ago
0
Test phasing with HapTree-X
#74
pontushojer
opened
12 months ago
0
Rule map_sort sometimes fails for ema
#73
pontushojer
opened
12 months ago
0
Remove tagbam for DBS and TELL-seq when mapping with EMA
#72
pontushojer
opened
12 months ago
0
Test alternative phasing algorithm: SpecHap
#71
pontushojer
opened
12 months ago
0
Update use of read groups
#70
pontushojer
opened
12 months ago
0
Snakemake version >=6.5 does not schedule jobs optimally
#69
pontushojer
opened
12 months ago
0
MultiQC 1.12 not compatible with BLR
#68
pontushojer
opened
12 months ago
0
gatk HaplotypeCaller filters out QUAL < 30 by default
#67
pontushojer
opened
12 months ago
0
Add Manta and MTG-Link for SV calling
#66
pontushojer
closed
9 months ago
0
Add support for integrating long reads
#65
pontushojer
closed
1 year ago
0
Use mambaforge directly
#64
pontushojer
closed
1 year ago
0
Additional phasing stats
#63
pontushojer
closed
1 year ago
0
fix CI
#62
pontushojer
closed
1 year ago
0
Update actions/checkout and actions/setup-python to latest
#61
pontushojer
closed
1 year ago
0
Do not lint on macOS
#60
marcelm
closed
2 years ago
1
Run macOS CI tests only on request
#59
marcelm
closed
2 years ago
0
Reduce number of scheduled CI runs
#58
marcelm
closed
2 years ago
2
Update blr run command to allow all snakemake arguments out-of-the-box
#57
pontushojer
closed
2 years ago
7
Reduce starcode memory use by pre-counting barcodes
#56
HSiga
closed
3 years ago
5
Start using actual lock-files for test-environments.
#55
pontushojer
closed
3 years ago
0
Update testdata to version 0.6
#54
pontushojer
closed
3 years ago
0
Multi threaded index_bam in run_anew.smk
#53
HSiga
closed
3 years ago
1
Introduce primary contigs
#52
pontushojer
closed
3 years ago
2
Basic profiling
#51
pontushojer
closed
3 years ago
0
Add DBS as library type and add depreciation warning for BLR
#50
pontushojer
closed
3 years ago
2
Split BLR FASTQ for ema mapping
#49
pontushojer
closed
3 years ago
0
Update CI and make snakemake logs richer
#48
pontushojer
closed
3 years ago
0
Phaseblock Ideogram
#47
pontushojer
closed
3 years ago
0
Map FASTQ bins directly for 10x input
#46
pontushojer
closed
3 years ago
0
Minor typos
#45
HSiga
closed
3 years ago
1
Linkedsv integration
#44
HSiga
closed
3 years ago
0
Linked sv
#43
HSiga
closed
3 years ago
2
Phase only diploid chromosomes
#42
pontushojer
closed
3 years ago
0
Integrate lariat an optional mapper
#41
pontushojer
closed
3 years ago
0
Add NAIBR for LSV calling
#40
pontushojer
closed
3 years ago
4
Update cluster duplicate calling
#39
pontushojer
closed
4 years ago
0
Check all YAML files for missing newlines at end of file
#38
marcelm
closed
4 years ago
1
Add sorting to tagfastq for direct ema formated output
#37
pontushojer
closed
4 years ago
1
Integrate lariat
#36
HSiga
closed
4 years ago
2
Enable running merging/rerunning previous runs
#35
pontushojer
closed
4 years ago
0
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