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Sync from bench #29

Merged
merged 30 commits into from
Apr 7, 2021
Merged

Sync from bench #29

merged 30 commits into from
Apr 7, 2021

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baraaorabi
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@baraaorabi
81683be
@baraaorabi
minor changes
a8f9898
@baraaorabi
including LTR-sim as submod
1f3efa1
@baraaorabi
upto mapping is automated
667abed
@baraaorabi
Fixed issue with where there are too many contigs
10de8a8
@baraaorabi
Snakefile is good; need to fix freddie_isoforms.py
43cffc6
@baraaorabi
isoform collapsing is done; reduced cluster noise
854bfbe
@baraaorabi
Generating transcripts and beds
3661688
@baraaorabi
Generating all baseline fastas and beds
04d0132
@baraaorabi
bugfix
fa9fe18
@baraaorabi
We have overlaps too
14d58f7
@baraaorabi
Done with running tools
1b3cdd1
@baraaorabi
rm files; edges are ready
a50549a
@baraaorabi
Bugfix
b70ee93
@baraaorabi
Accuracy ploting
772ed12
@baraaorabi
accuracy integrated into snakemake
d8b5907
@baraaorabi
fully specified env add
8ff243e
@baraaorabi
Merge branch 'benchmarking' of https://github.com/vpc-ccg/freddie int…
6239af6 
…o benchmarking

Conflicts:
	benchmark_config.yaml
@baraaorabi
removed prefix from env
6203ab0
@baraaorabi
Split conda envs, all working till gtime now
cc46660
@baraaorabi
Made a switch to parallel for mini tasks
0a4a820
@baraaorabi
fix in fa gen; acc py gens dirs; acc sm in gpara
2b7b922
@baraaorabi
bugfix for baseline acc
d00ca5e
@baraaorabi
Delete .gitmodules
c95d3ba
@baraaorabi
Delete Snakefile-accuracy
36abb00
@baraaorabi
Delete accuracy.yml
021a0aa
@baraaorabi
Delete flair.yml
d1f6449
@baraaorabi
Delete run_tools.yml
cacafa0
@baraaorabi
restore Snakefile
e057b87
baraaorabi
baraaorabi commented Apr 7, 2021
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Looking good

@baraaorabi baraaorabi merged commit 8bbca68 into master Apr 7, 2021
@baraaorabi baraaorabi deleted the sync_from_bench branch April 7, 2021 17:26
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@baraaorabi