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feat: upgrade to Snakemake version 9

enhancementNew feature or requestNew feature or request

Status: Open.

Feature

#190 In zavolanlab/zarp;

· fgypas opened on Jul 13, 2025

changelog notes protected branch

bugSomething isn't workingSomething isn't working

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#129 In zavolanlab/zarp;

· mkatsanto opened on Mar 30, 2023

feat: RO-crate packaging of workflow and metadata

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#120 In zavolanlab/zarp;

· ninsch3000 opened on Mar 10, 2023

chore: Move function definitions from top of Snakefile to separate module

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#119 In zavolanlab/zarp;

· ninsch3000 opened on Mar 10, 2023

feat: replace BAM by CRAM format

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#118 In zavolanlab/zarp;

· ninsch3000 opened on Mar 10, 2023

feat: add support for cloud execution

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#117 In zavolanlab/zarp;

· ninsch3000 opened on Mar 10, 2023

feat: Remove PCR duplicates

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#116 In zavolanlab/zarp;

· ninsch3000 opened on Mar 10, 2023

feat: support GTF formats other than ensembl

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#115 In zavolanlab/zarp;

· ninsch3000 opened on Mar 10, 2023

test: automate end-to-end testing

futurewill not be fixed for NOWwill not be fixed for NOW

testingtest runs or similartest runs or similar

Status: Open.

#85 In zavolanlab/zarp;

· mkatsanto opened on Oct 28, 2022

Scale time resources

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#59 In zavolanlab/zarp;

· mkatsanto opened on Mar 16, 2022

Normalize results by fraction of reads in some MultiQC plots

enhancementNew feature or requestNew feature or request

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#36 In zavolanlab/zarp;

· uniqueg opened on Nov 16, 2021

Support for unstranded data

enhancementNew feature or requestNew feature or request

futurewill not be fixed for NOWwill not be fixed for NOW

Status: Open.

#32 In zavolanlab/zarp;

· dominikburri opened on Nov 5, 2021