Code

adding viloca to the workflow#150

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DrYak merged 89 commits intomastercbg-ethz/V-pipe:masterfrom add_vilocacbg-ethz/V-pipe:add_vilocaCopy head branch name to clipboardJun 7, 2024

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Commits on Jun 4, 2024

• Version bump COJAC 0.9.2

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Commits on Jun 7, 2024

• [method] cliquesnv with output snvs -- create empyt file if cliquesnv is not outputting anything

  

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• exclude shorah_amplicon since it fails on the illumina populations due to an error in b2w

  

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• vary population parameters and coverage

  

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• subsample hiv mix

  

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• exlcude viloca_multi since the cluster allocation of multiple threads sort of didn't work

  

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• add rerun-triggers mtime snakemake command

  

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• [viloca] set higher win_min_ext threshold for 10-IAV-mix

  

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• updates

  

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• conda enviroment

  

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• viloca with older configuration

  

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• exclude indels configuration for now

  

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• PVY mix with uniform tiling

  

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• add another sars-mix

  

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• update resources

  

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• add older viloca configuration

  

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• more methods + updated populations

  

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• run indel also

  

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• rename methods, since bash takes files names of length max 255

  

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• method names updated

  

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• method names updated

  

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• b2w multi

  

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• fix: in case no mutations are in vcf

  

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• [update] distance populations for conference figures

  

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• [viloca method] also report posterior of haplotypes

  

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• [varyvilocaparams] update config and params

  

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• [realdata] don't use SARS-CoV-2-Two-Strain-Mix -- since we don't have the full ground truth

  

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• [HIV-5-mix] update ground truth - exclude deletions since they are no biological deletions but rather due to incomplete reference strains

  

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• [single_bed_file] fix

  

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• [single_bed_file] fix int

  

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• [performance_global] save posterior of predictions

  

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• [method_def] viloca with posterior threshold

  

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• [method_def] viloca with posterior threshold

  

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• [experimental data] 5-virus-mix correct ground truth

  

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• [local_haplo] add predicthaplo

  

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• add method: strainline

  

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• update method strainline

  

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• update method strainline

  

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• remove rules for 2 strain sars-cov2 mix

  

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• add predicthaplo

  

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• remove old methods that are not used anywhere

  

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• correct output name for different applications and improved comments

  

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• [shorah] reduce window size for illumina samples

  

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• [fix] simulation of deletions and insertions into the haplotypes

  

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• [add] extra performance measures for local_haplo_setup

  

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• fix illumina simulation with indels in haplotypes, bwa is not aligning them correctly, hence use minimap2

  

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• fix indel simulation, ground truth table, simulate missing codon or inserted codon

  

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• [remove] rule to provide curlcakes ont data

  

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• [remove] rule to provide wastewater sars-cov2 data

  

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• [remove] rule to provide wastewater sars-cov2 data

  

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• [remove] rule to provide wastewater sars-cov2 data

  

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• [remove] rule to provide wastewater sars-cov2 data

  

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• [fix groud truth list for distance haplo generation]

  

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• [clean-up] ground_truth_corrected.csv not neeeded anymore, since ground_truth.csv was fixed

  

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• config_distance: final version as in manuscript

  

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• remove cliquesnv version that returns snvs wrt consensus seq

  

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• distance config: final methods

  

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• remove corrected groundtruth file

  

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• final methods list and simulated dataset for varyvilocaparams

  

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• realdata update to final method versions

  

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• call indels

  

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• remove outdated methods

  

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• method_definitions: cliquesnv

  

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• update method defintions as run on cluster

  

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• generate haplotypes: correct deletion position in ground truth

  

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• [local_haplo_setup] add readme

  

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• fix indel ground truth and performance evaluationa

  

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• fix indel ground truth and performance evaluationa

  

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• indel config

  

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• remove isfile() tst

  

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• update viloca ewm for amplicon

  

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• add indel settings and performance eval

  

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• typo

  

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• [real data] complete insert file

  

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• [add] notebooks for figures in manuscript

  

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• Keep the linter happy

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• adding viloca to the workflow

  

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• fix file paths

  

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• update conig_schema

  

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• adding paired_end_read_merger

  

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• update rule for paired_en_read_merger + add conda env definition

  

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• update rule for paired_en_read_merger + add conda env definition

  

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• update enviroment

  

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• add paired_end_read_merger

  

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• update paired_end_read_merger rule

  

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• add conda package to env

  

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• Viloca touch ups

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• Linting

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• Generate copnfig manual

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