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Cleanup command line interfaces

Status: Open.

#56 In marschall-lab/strand-seq-graph-phasing;

· mir-cat opened on Jan 3, 2025

Error in rule count_haplotype_markers

Status: Open.

#54 In marschall-lab/strand-seq-graph-phasing;

· nidhi12k opened on Sep 24, 2024

Identify "true" misorientations by comparing edges to and from nodes with their Strand-seq inferred orientation

Status: Open.

#51 In marschall-lab/strand-seq-graph-phasing;

· mir-cat opened on Apr 15, 2024

Convert short R scripts to inline code?

Status: Open.

#50 In marschall-lab/strand-seq-graph-phasing;

· mir-cat opened on Apr 4, 2024

What parameters to expose in config file?

Status: Open.

#49 In marschall-lab/strand-seq-graph-phasing;

· mir-cat opened on Apr 4, 2024

Refactor rule inputs to use rules.[rule name].output.[output name] format

Status: Open.

#37 In marschall-lab/strand-seq-graph-phasing;

· mir-cat opened on Nov 27, 2023

Improve phasing information transfer from pipeline to hifiasm

Status: Open.

#35 In marschall-lab/strand-seq-graph-phasing;

· mir-cat opened on Nov 14, 2023