Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Updated benchmark #156

Open
wants to merge 74 commits into
base: master
Choose a base branch
from
Open

Updated benchmark #156

wants to merge 74 commits into from

Conversation

LaraFuhrmann
Copy link
Collaborator

Added Benchmark study for VILOCA to the benchmarking.

@LaraFuhrmann
[method] cliquesnv with output snvs -- create empyt file if cliquesnv…
b287705 
… is not outputting anything
@LaraFuhrmann
exclude shorah_amplicon since it fails on the illumina populations du…
c4fdcf0 
…e to an error in b2w
@LaraFuhrmann
vary population parameters and coverage
cfbaffc
@LaraFuhrmann
subsample hiv mix
45ce842
@LaraFuhrmann
exlcude viloca_multi since the cluster allocation of multiple threads…
c97da1b 
… sort of didn't work
@LaraFuhrmann
add rerun-triggers mtime snakemake command
ba84c18
@LaraFuhrmann
[viloca] set higher win_min_ext threshold for 10-IAV-mix
d99418d
@LaraFuhrmann
updates
8cad328
@LaraFuhrmann
conda enviroment
938e2c7
@LaraFuhrmann
viloca with older configuration
2b20219
@LaraFuhrmann
exclude indels configuration for now
be57d3e
@LaraFuhrmann
PVY mix with uniform tiling
d65ec6d
@LaraFuhrmann
add another sars-mix
f9cc7a5
@LaraFuhrmann
update resources
fe9be44
@LaraFuhrmann
add older viloca configuration
9795475
@LaraFuhrmann
more methods + updated populations
9872a2b
@LaraFuhrmann
run indel also
62b15d1
@LaraFuhrmann
rename methods, since bash takes files names of length max 255
d4763ac
@LaraFuhrmann
method names updated
0f21883
@LaraFuhrmann
method names updated
892d514
@LaraFuhrmann
b2w multi
d09e57b
@LaraFuhrmann
fix: in case no mutations are in vcf
e0f8817
@LaraFuhrmann
[update] distance populations for conference figures
4d79916
@LaraFuhrmann
[viloca method] also report posterior of haplotypes
807e63c
@LaraFuhrmann
[varyvilocaparams] update config and params
47e8948
@LaraFuhrmann
[realdata] don't use SARS-CoV-2-Two-Strain-Mix -- since we don't have…
1d98c63 
… the full ground truth
@LaraFuhrmann
[HIV-5-mix] update ground truth - exclude deletions since they are no…
d1fd7de 
… biological deletions but rather due to incomplete reference strains
@LaraFuhrmann
[single_bed_file] fix
eef40b0
@LaraFuhrmann
[single_bed_file] fix int
2147d7b
@LaraFuhrmann
[performance_global] save posterior of predictions
2effca5
@LaraFuhrmann
fix indel simulation, ground truth table, simulate missing codon or i…
a9e1bfb 
…nserted codon
@LaraFuhrmann
[remove] rule to provide curlcakes ont data
dde0cf0
@LaraFuhrmann
[remove] rule to provide wastewater sars-cov2 data
d1b46c3
@LaraFuhrmann
[remove] rule to provide wastewater sars-cov2 data
39cf244
@LaraFuhrmann
[remove] rule to provide wastewater sars-cov2 data
f35a0d7
@LaraFuhrmann
[remove] rule to provide wastewater sars-cov2 data
70cb658
@LaraFuhrmann
[fix groud truth list for distance haplo generation]
93b6333
@LaraFuhrmann
[clean-up] ground_truth_corrected.csv not neeeded anymore, since grou…
7ccfc74 
…nd_truth.csv was fixed
@LaraFuhrmann
config_distance: final version as in manuscript
8c2bc2b
@LaraFuhrmann
remove cliquesnv version that returns snvs wrt consensus seq
7988f1b
@LaraFuhrmann
distance config: final methods
62d5a28
@LaraFuhrmann
remove corrected groundtruth file
4aae352
@LaraFuhrmann
final methods list and simulated dataset for varyvilocaparams
3f47a38
@LaraFuhrmann
realdata update to final method versions
a160177
@LaraFuhrmann
call indels
6f8d2bc
@LaraFuhrmann
remove outdated methods
a79aca6
@LaraFuhrmann
method_definitions: cliquesnv
bb333b3
@LaraFuhrmann
update method defintions as run on cluster
bbfe604
@LaraFuhrmann
generate haplotypes: correct deletion position in ground truth
db64230
@LaraFuhrmann
[local_haplo_setup] add readme
88a6388
@LaraFuhrmann
fix indel ground truth and performance evaluationa
27ef96e
@LaraFuhrmann
fix indel ground truth and performance evaluationa
1269522
@LaraFuhrmann
indel config
3711f38
@LaraFuhrmann
remove isfile() tst
c3553eb
@LaraFuhrmann
update viloca ewm for amplicon
1b78793
@LaraFuhrmann
add indel settings and performance eval
9f20d9c
@LaraFuhrmann
typo
bb72732
@LaraFuhrmann
[real data] complete insert file
f0fed69
@LaraFuhrmann
[add] notebooks for figures in manuscript
54dd6de
@github-actions GitHub Actions
Copy link

🦙 MegaLinter status: ❌ ERROR

Descriptor Linter Files Fixed Errors Elapsed time
✅ BASH shellcheck 11 0 0.96s
✅ DOCKERFILE hadolint 1 0 0.37s
✅ JUPYTER jupyfmt 11 8 0 7.17s
❌ MARKDOWN markdownlint 12 1 6 1.17s
✅ PERL perlcritic 1 0 1.28s
❌ PYTHON black 52 18 1 2.96s
✅ SNAKEMAKE snakefmt 25 2 0 10.5s

See detailed report in MegaLinter reports

MegaLinter is graciously provided by OX Security

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.

None yet
1 participant
@LaraFuhrmann