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Outdated quick_install.sh in the Installation guide

help wanted

Status: Open.

#188 In cbg-ethz/V-pipe;

· mcavegn opened on Oct 25, 2025

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

help wanted

Status: Open.

#187 In cbg-ethz/V-pipe;

· poursalavati opened on Oct 20, 2025

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

help wanted

Status: Open.

#186 In cbg-ethz/V-pipe;

· poursalavati opened on Oct 20, 2025

Version-bump all dependencies

enhancement

Status: Open.

Feature

#185 In cbg-ethz/V-pipe;

· DrYak opened on Sep 18, 2025

Replace XSV as it is NOT maintained anymore

enhancement

Status: Open.

Feature

#184 In cbg-ethz/V-pipe;

· DrYak opened on Sep 18, 2025

Make content of resource/ world writeable in Docker

bug

Status: Open.

#183 In cbg-ethz/V-pipe;

· DrYak opened on Sep 10, 2025

Basecount rule is taking more than 24hrs

help wanted

Status: Open.

#182 In cbg-ethz/V-pipe;

· JigarHSheth opened on Aug 2, 2025

Error in running the pipeline

Status: Open.

#181 In cbg-ethz/V-pipe;

· JigarHSheth opened on Jul 21, 2025

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

enhancement

help wanted

Status: Open.

#176 In cbg-ethz/V-pipe;

· gordonkoehn opened on Apr 25, 2025

HIV workflow error

Status: Open.

#168 In cbg-ethz/V-pipe;

· antoine4ucsd opened on Dec 28, 2024

Default deconvolution config is missing

help wanted

Status: Open.

#161 In cbg-ethz/V-pipe;

· GeertvanGeest opened on Sep 13, 2024

Workflow error from V-pipe dry run

help wanted

Status: Open.

#160 In cbg-ethz/V-pipe;

· robertsap opened on Sep 9, 2024