Commits on Sep 6, 2024

1. update feature-benchmark branch (#158) …

   * adding viloca to the workflow
   
   * fix file paths
   
   * update conig_schema
   
   * adding paired_end_read_merger
   
   * update rule for paired_en_read_merger + add conda env definition
   
   * update rule for paired_en_read_merger + add conda env definition
   
   * update enviroment
   
   * add paired_end_read_merger
   
   * update paired_end_read_merger rule
   
   * add conda package to env
   
   * Viloca touch ups
   
   - snakemake handles `directory()`
   - VILOCA 1.0.0 on bioconda
   - use GitLab for smallgenomeutilites due to GitHub LFS limitations
   
   * Linting
   
   * Generate copnfig manual
   
   * Documentation touch ups
   
   - update paper: V-pipe 3.0 pre-print
   - WorkflowHub's required documentation.md points to our documentation
   - Update Tutorial intro page: point to installer
   
   * improve tutorial_0_install.md
   
   * Links to bioconda in installation tutorial
   
   * Singularity+conda support
   
   * Update README.md  with viloca reference
   
   * Add issue templates
   
   * Contributing guidelines
   
   * Disable linter for templates
   
   * bugfix: viloca
   
   - typo fix
   - all: depends on correct CSV
   
   * bugfix: bump versions of bcftools and cyvcf2
   
   - recent change of numpy in bioconda breaks older cyvcf
   
   * [bump] LolliPop 0.4.0
   
   - support new `filters` option
   
   * Update of conf manual
   
   * [bump] LolliPop v0.4.1
   
   ---------
   
   Co-authored-by: Ivan Blagoev Topolsky <[email protected]>
   Co-authored-by: Prajwal Kulkarni <[email protected]>
   Co-authored-by: Ivan Blagoev Topolsky <[email protected]>

   

   4 people authored Sep 6, 2024
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2. update modules to load for new ubuntu system

   

   LaraFuhrmann committed Sep 6, 2024
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3. add rule to run haplodmf -- due to conflicts in python version we can… …

   …not run it as python script

   

   LaraFuhrmann committed Sep 6, 2024
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4. extend simulation scenarios and methods list

   

   LaraFuhrmann committed Sep 6, 2024
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5. add haploflow

   

   LaraFuhrmann committed Sep 6, 2024
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6. add notebook for new figure

   

   LaraFuhrmann committed Sep 6, 2024
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