Quasispecies Reconstruction Benchmark#115

Merged

DrYak merged 527 commits intomasterfrom feature-benchmark

Oct 13, 2023

+180,855-1,268

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Commits on Jul 19, 2022

Commits on Jul 20, 2022

[update] benchmark settings for local_haplo_setup
Lara Fuhrmann
committed
[update]methods for local_haplo_setup
Lara Fuhrmann
committed
[added] lofreq to the benchmark methods
Lara Fuhrmann
committed
[local_haplotype_setup] config correction
Lara Fuhrmann
committed
[local_haplotype_setup] correction
Lara Fuhrmann
committed
correct version
Lara Fuhrmann
committed
some updates
Lara Fuhrmann
committed
[local_haplotype_setup] added run status
Lara Fuhrmann
committed

Commits on Jul 21, 2022

[local_haplotype_setup] correction config
Lara Fuhrmann
committed
[local_haplotype_setup] correction
Lara Fuhrmann
committed
[local_haplotype_setup] change of alpha in shorah method
Lara Fuhrmann
committed
[local_haplotype_setup] higher memory for realdata setup
Lara Fuhrmann
committed
[local_haplotype_setup] realdata config
Lara Fuhrmann
committed

Commits on Jul 22, 2022

[local_haplotype_setup] increase resources for run method
Lara Fuhrmann
committed

Commits on Jul 25, 2022

[local_haplotype_setup] config_realdata -- subsampling
Lara Fuhrmann
committed
[local_haplotype_setup] update methods in config files
Lara Fuhrmann
committed
[local_haplotype_setup] config for long reads
Lara Fuhrmann
committed
[local_haplotype_setup] added amplicon illumina simulaation, adapted methods for that
Lara Fuhrmann
committed
[local_haplotype_setup] running full benchmark for all configs
Lara Fuhrmann
committed

Commits on Jul 26, 2022

Use conda function to dynamically generate conda envs
kpj
committed
Integration of cowwid amplicon benchmarking data
Lara Fuhrmann
committed
[local_haplotype_setup] add benchmarking on real data SARS-CoV-2 2-strain mix
Lara Fuhrmann
committed

Commits on Aug 3, 2022

initial steps for general tutorial
Lara Fuhrmann
committed

Commits on Aug 4, 2022

[local_haplotype_setup] long reads config -- correction in performance_global
Lara Fuhrmann
committed

Commits on Aug 5, 2022

[local_haplotype_setup] correction in performance_measures_global
Lara Fuhrmann
committed
[local_haplotype_setup] Add - config_realdata_sarscov2
Lara Fuhrmann
committed
[local_haplotype_setup] integration of config_realdata_SARS_CoV2
Lara Fuhrmann
committed
[local_haplotype_setup] update configurations
Lara Fuhrmann
committed

Commits on Aug 6, 2022

[local_haplotype_setup] correction
Lara Fuhrmann
committed

Commits on Aug 12, 2022

Commits on Aug 15, 2022

[local_haplotype_setup] method defitinions
Lara Fuhrmann
committed
Fix spurious symlinks in upload subdirectories

uweschmitt
authored and
DrYak
committed
Fix snakemake 7.11 not grouping pipe
DrYak
committed
BAM trimming according to primers with ivar, new rule

Michal Okoniewski
authored and
DrYak
committed
Adapting primer trimming
DrYak
committed
Modernise tests
DrYak
committed
Ignore secondary and supplementary for dehuman count
DrYak
committed
Fix typos in config
DrYak
committed
Per-sample protocol
DrYak
committed
New configuration options
DrYak
committed
Logging
DrYak
committed
Primers samtools and per-sample
DrYak
committed
Primers trimming wired in
DrYak
committed
Sanity checks: 4 columns and primers
DrYak
committed

Commits on Aug 16, 2022

Commits on Aug 17, 2022

Documentation
DrYak
committed

Commits on Aug 18, 2022

[local_haplotype_setup] update config and methods
Lara Fuhrmann
committed

Commits on Aug 22, 2022

[updated]
Lara Fuhrmann
committed

Commits on Aug 24, 2022

[long read simulation] use minimap2 as aligner
Lara Fuhrmann
committed
[local_haplotyep_setup] Add test config
Lara Fuhrmann
committed
[long read simulation] fix minimap2 alignment
Lara Fuhrmann
committed
[local_haplotype_setup] update config + test specific run_method rule
Lara Fuhrmann
committed
Config validation user friendliness
DrYak
committed

Commits on Aug 25, 2022

[local_haplotype_setup] integration of curlcakes_ONT data
Lara Fuhrmann
committed
[local_haplotype_setup] integration of curlcakes_ONT data
Lara Fuhrmann
committed
[local_haplotype_setup] integration of curlcakes_ONT data
Lara Fuhrmann
committed
quast things optional
Lara Fuhrmann
committed
save false positives for cases where there are no mutations in ground truth
Lara Fuhrmann
committed
[local_haplotype_setup] don't run quast for global measures
Lara Fuhrmann
committed
quast running for global measures + adaptation paths for curlcakes ONT data
Lara Fuhrmann
committed
[local_haplotype_setup] params for run_method
Lara Fuhrmann
committed
[curlcakes_ONT] change params.csv
Lara Fuhrmann
committed

Commits on Aug 26, 2022

[haplotypes_stats] add exception for coverage not being float
Lara Fuhrmann
committed
[performance_measures_local] fix for false_postives reporting
Lara Fuhrmann
committed

Commits on Sep 6, 2022

..
Lara Fuhrmann
committed
[Added] snv-ground-truth for the Five-Virus-Mix
Lara Fuhrmann
committed
[local-haplotype-setup] Two-strain-SARS-CoV-2 mix
Lara Fuhrmann
committed
[local_haplotype_setup] update configs for new method_definitions
Lara Fuhrmann
committed
[local_haplotype_setup] update methods defintion for amplicon version
Lara Fuhrmann
committed
[Add] local_haplotype_setup methods to general config
Lara Fuhrmann
committed
[local_haplotype_setup] long reads config update
Lara Fuhrmann
committed

Commits on Sep 7, 2022

[fix] population nucleotide diversity
Lara Fuhrmann
committed

Commits on Sep 8, 2022

[local_haplotype_setup] update params
Lara Fuhrmann
committed
[fix] indent
Lara Fuhrmann
committed
[performance_measures_global] quast as optional -- quast not needed for local haplotypes
Lara Fuhrmann
committed

Commits on Sep 13, 2022

[mds plots]different markers for different methods
Lara Fuhrmann
committed

Commits on Sep 18, 2022

[update+add] added example HIV data, updated tutorial
Lara Fuhrmann
committed
smallcorrections
Lara Fuhrmann
committed
smallcorrections
Lara Fuhrmann
committed
smallcorrections
Lara Fuhrmann
committed

Commits on Sep 30, 2022

1-base vs 0-based ; IDs with '/' or '-'

DrYak
authored and
Beerenwinkel TechnicalIdentity
committed
Support protocol look-up for jobinfo massimport

DrYak
authored and
Beerenwinkel TechnicalIdentity
committed
Support absent/deleted raw_data directory
DrYak
committed
Documentation update
DrYak
committed

Commits on Oct 1, 2022

Commits on Oct 2, 2022

Tutorial run their own branch of V-pipe
DrYak
committed
Fix: also use branch's installer in tutorials
DrYak
committed
[fix] populatin_nucleotide_diversity

Lara Fuhrmann
authored and
DrYak
committed
Fixing path for LAra's workshop
DrYak
committed

Commits on Oct 4, 2022

include trimming and uploads among default config
DrYak
committed

Commits on Oct 5, 2022

Commits on Oct 6, 2022

Fix: sample table's column (len)
DrYak
committed

Commits on Oct 27, 2022

Version bump smallgenomeutilities
DrYak
committed

Commits on Dec 14, 2022

Commits on Dec 16, 2022

Commits on Dec 19, 2022

corrected import of package
LaraFuhrmann
committed

Commits on Jan 10, 2023

[local_haplotype_setup] correct params for PVY data
LaraFuhrmann
committed

Commits on Jan 12, 2023

add method definition
LaraFuhrmann
committed

Commits on Jan 31, 2023

Commits on Mar 8, 2023

typo in ground truth path
LaraFuhrmann
committed

Commits on Mar 10, 2023

Commits on Mar 14, 2023

PVY real_data: better window definition
LaraFuhrmann
committed

Commits on Apr 3, 2023

Commits on Apr 18, 2023

Commits on Apr 25, 2023

added other sars data
LaraFuhrmann
committed

Commits on May 15, 2023

Commits on May 31, 2023

Commits on Jun 19, 2023

[add]viloca_envp
LaraFuhrmann
committed

Commits on Jul 20, 2023

update params since otherwise freq is too low
LaraFuhrmann
committed

Commits on Jul 21, 2023

fix
LaraFuhrmann
committed

Commits on Aug 11, 2023

Commits on Aug 12, 2023

update configs and runtime
LaraFuhrmann
committed

Commits on Aug 27, 2023

[update] package version - conflict with python and samtools version
LaraFuhrmann
committed

Commits on Sep 8, 2023

[benchmarking_tutorial] change coverage to 1000
LaraFuhrmann
committed

Commits on Sep 12, 2023

Commits on Oct 6, 2023

[indels] update method run file with threads and without haplo files
LaraFuhrmann
committed

Commits on Oct 11, 2023

[performance_global] add second csv with 0.005 threshold for true postives
LaraFuhrmann
committed