Issues

• Outdated quick_install.sh in the Installation guide

  help wanted
  cbg-ethz/V-pipe#188 · Filter by author mcavegn opened on Oct 25, 2025

• Bug: Incorrect shell command syntax in basecounts_QC rule (mafs.smk)

  help wanted
  cbg-ethz/V-pipe#187 · Filter by author poursalavati opened on Oct 20, 2025
  1

  

• Bug: Bowtie2 v2.4.1 produces malformed BAM headers causing downstream failures

  help wanted
  cbg-ethz/V-pipe#186 · Filter by author poursalavati opened on Oct 20, 2025
  1

  

• Version-bump all dependencies

  enhancement
  Feature

  cbg-ethz/V-pipe#185 · Filter by author DrYak opened on Sep 18, 2025
  

• Replace XSV as it is NOT maintained anymore

  enhancement
  Feature

  cbg-ethz/V-pipe#184 · Filter by author DrYak opened on Sep 18, 2025
  

• Make content of resource/ world writeable in Docker

  bug
  cbg-ethz/V-pipe#183 · Filter by author DrYak opened on Sep 10, 2025
  

• Basecount rule is taking more than 24hrs

  help wanted
  cbg-ethz/V-pipe#182 · Filter by author JigarHSheth opened on Aug 2, 2025
  5

  

• Error in running the pipeline

  cbg-ethz/V-pipe#181 · Filter by author JigarHSheth opened on Jul 21, 2025
  3

  

• sra-tools command line tool: missing from Sars-Cov-2 Tutorial instructions

  enhancementhelp wanted
  cbg-ethz/V-pipe#176 · Filter by author gordonkoehn opened on Apr 25, 2025
  1

• HIV workflow error

  cbg-ethz/V-pipe#168 · Filter by author antoine4ucsd opened on Dec 28, 2024
  18

  

• Default deconvolution config is missing

  help wanted
  cbg-ethz/V-pipe#161 · Filter by author GeertvanGeest opened on Sep 13, 2024

• Workflow error from V-pipe dry run

  help wanted
  cbg-ethz/V-pipe#160 · Filter by author robertsap opened on Sep 9, 2024
  4

  

• Setting VILOCA --windowsize parameter using v-pipe config file not possible

  help wanted
  cbg-ethz/V-pipe#157 · Filter by author anikajohn opened on Jul 18, 2024

• Problem in the deconvolution step

  cbg-ethz/V-pipe#148 · Filter by author Xuyen21 opened on Jan 8, 2024
  4

  

• Activating snv in sars tutorial leads to error

  cbg-ethz/V-pipe#146 · Filter by author schlaepferp opened on Jun 13, 2023
  2

  

• Missing input files for rule generate_web_visualization

  cbg-ethz/V-pipe#139 · Filter by author carlottaolivero opened on Mar 8, 2023

• Error in rule hmm_align: HIV in Vpipe

  cbg-ethz/V-pipe#138 · Filter by author vfdiamante opened on Feb 2, 2023
  2

• hiv-tutorial fails with haplotype_reconstruction: savage, and SAVAGE command output is dumped into terminal instead of log

  cbg-ethz/V-pipe#137 · Filter by author Masterxilo opened on Nov 18, 2022

• hiv-tutorial works with haploclique, but fails with predicthaplo

  cbg-ethz/V-pipe#136 · Filter by author Masterxilo opened on Nov 18, 2022

• [UX issue] multiple GFF

  cbg-ethz/V-pipe#134 · Filter by author DrYak opened on Nov 4, 2022
  1

• [UX issue] unknown keywords in config file

  cbg-ethz/V-pipe#133 · Filter by author DrYak opened on Nov 4, 2022
  1

• Warning: All reads at position 4045 in the same reverse orientation ?

  cbg-ethz/V-pipe#126 · Filter by author Vinoy-UKHSA opened on Mar 16, 2022
  1

  

• SARS-CoV-2 workflow comparison - kindly check if your work is represented correctly

  cbg-ethz/V-pipe#124 · Filter by author thomasbtf opened on Mar 7, 2022
  1

  

• please document haploclique.extra_parameters

  cbg-ethz/V-pipe#122 · Filter by author Masterxilo opened on Feb 4, 2022
  3

• Getting snake error

  cbg-ethz/V-pipe#120 · Filter by author dstcr opened on Jan 22, 2022
  23