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Updated benchmark #156

Merged
merged 76 commits into from
Jun 7, 2024
Merged

Updated benchmark #156

merged 76 commits into from
Jun 7, 2024

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LaraFuhrmann
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Added Benchmark study for VILOCA to the benchmarking.

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github-actions bot commented May 13, 2024 •
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@LaraFuhrmann LaraFuhrmann requested a review from DrYak June 6, 2024 12:42
@LaraFuhrmann
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This branch is ready to be merged. @DrYak

@LaraFuhrmann @DrYak
[method] cliquesnv with output snvs -- create empyt file if cliquesnv…
34a3e36 
… is not outputting anything
@LaraFuhrmann @DrYak
exclude shorah_amplicon since it fails on the illumina populations du…
c6e555d 
…e to an error in b2w
@LaraFuhrmann @DrYak
vary population parameters and coverage
66a0d0a
@LaraFuhrmann @DrYak
subsample hiv mix
ee6ddf8
@LaraFuhrmann @DrYak
exlcude viloca_multi since the cluster allocation of multiple threads…
d5733fc 
… sort of didn't work
@LaraFuhrmann @DrYak
add rerun-triggers mtime snakemake command
671d37e
@LaraFuhrmann @DrYak
[viloca] set higher win_min_ext threshold for 10-IAV-mix
de4354e
@LaraFuhrmann @DrYak
updates
960fa5b
@LaraFuhrmann @DrYak
conda enviroment
5a87288
@LaraFuhrmann @DrYak
viloca with older configuration
a322f7b
@LaraFuhrmann @DrYak
exclude indels configuration for now
193b691
@LaraFuhrmann @DrYak
PVY mix with uniform tiling
8ae9839
@LaraFuhrmann @DrYak
add another sars-mix
c6f221f
@LaraFuhrmann @DrYak
update resources
ef801f4
@LaraFuhrmann @DrYak
add older viloca configuration
92e34db
@LaraFuhrmann @DrYak
more methods + updated populations
24432ad
@LaraFuhrmann @DrYak
run indel also
0d57c99
@LaraFuhrmann @DrYak
rename methods, since bash takes files names of length max 255
bbd0355
@LaraFuhrmann @DrYak
method names updated
709bcf7
@LaraFuhrmann @DrYak
method names updated
035b154
@LaraFuhrmann @DrYak
b2w multi
e33697b
@LaraFuhrmann @DrYak
fix: in case no mutations are in vcf
3ec6395
@LaraFuhrmann @DrYak
[update] distance populations for conference figures
a27917d
@LaraFuhrmann @DrYak
[viloca method] also report posterior of haplotypes
d92d46b
@LaraFuhrmann @DrYak
[varyvilocaparams] update config and params
9410d2b
@LaraFuhrmann @DrYak
[realdata] don't use SARS-CoV-2-Two-Strain-Mix -- since we don't have…
4f6d22d 
… the full ground truth
@LaraFuhrmann @DrYak
[remove] rule to provide wastewater sars-cov2 data
b3123ac
@LaraFuhrmann @DrYak
[remove] rule to provide wastewater sars-cov2 data
4bfc2d6
@LaraFuhrmann @DrYak
[remove] rule to provide wastewater sars-cov2 data
3eade89
@LaraFuhrmann @DrYak
[fix groud truth list for distance haplo generation]
7223f86
@LaraFuhrmann @DrYak
[clean-up] ground_truth_corrected.csv not neeeded anymore, since grou…
26ddd53 
…nd_truth.csv was fixed
@LaraFuhrmann @DrYak
config_distance: final version as in manuscript
5fba0ba
@LaraFuhrmann @DrYak
remove cliquesnv version that returns snvs wrt consensus seq
b29db53
@LaraFuhrmann @DrYak
distance config: final methods
2c5f604
@LaraFuhrmann @DrYak
remove corrected groundtruth file
fb55348
@LaraFuhrmann @DrYak
final methods list and simulated dataset for varyvilocaparams
32265a2
@LaraFuhrmann @DrYak
realdata update to final method versions
f595971
@LaraFuhrmann @DrYak
call indels
fb54a42
@LaraFuhrmann @DrYak
remove outdated methods
2804035
@LaraFuhrmann @DrYak
method_definitions: cliquesnv
40bea26
@LaraFuhrmann @DrYak
update method defintions as run on cluster
d76f40d
@LaraFuhrmann @DrYak
generate haplotypes: correct deletion position in ground truth
d7cc318
@LaraFuhrmann @DrYak
[local_haplo_setup] add readme
7814934
@LaraFuhrmann @DrYak
fix indel ground truth and performance evaluationa
c5fbce1
@LaraFuhrmann @DrYak
fix indel ground truth and performance evaluationa
a388f4e
@LaraFuhrmann @DrYak
indel config
c533f17
@LaraFuhrmann @DrYak
remove isfile() tst
ebe53e5
@LaraFuhrmann @DrYak
update viloca ewm for amplicon
00ed959
@LaraFuhrmann @DrYak
add indel settings and performance eval
1b257c0
@LaraFuhrmann @DrYak
typo
56ff76d
@LaraFuhrmann @DrYak
[real data] complete insert file
21977cd
@LaraFuhrmann @DrYak
[add] notebooks for figures in manuscript
04ca094
@DrYak DrYak merged commit 9ab7264 into master Jun 7, 2024
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@LaraFuhrmann @DrYak