fix: fastplong wired in workflow and expose tool args

[m-jahn]

closes #46

[github-actions]

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[Copilot]

Copilot review overview

🟡 Changes recommended

STAR alignment input expansion currently enumerates all samples (breaking per-sample execution), and the new plotCoverage config access can raise KeyError with valid configs unless a safe default/requirement is enforced.

Review effort: Lite
Findings: 1 · 1 · 1

Open (3)

• STAR expand binds all samples instead of per-sample wildcard · New
• Missing deeptools_plotcoverage.extra can trigger KeyError · New
• Use WorkflowError and logger instead of SystemExit/print · New

What changed in this PR

This PR wires the selected read-processing tool (e.g., fastp vs fastplong) into downstream mapping rules by parameterizing input paths, and exposes DeepTools plotCoverage extra arguments via config (closing #46).

Changes:

• Update aligner rules (STAR/minimap2/bwa-mem2/bowtie2) to read processed FASTQs from results/{processing_tool}/... based on config["processing"]["tool"].
• Expose deeptools_plotcoverage extra CLI args via config + schema, and set defaults in example configs.
• Add workflow-time guardrails/warnings for unsupported tool/input combinations (fastplong + paired-end, minimap2 + paired-end warning).

File	Description
workflow/​rules/​star.smk	Switch STAR inputs to use the configured processing tool output directory.
workflow/​rules/​minimap2.smk	Parameterize minimap2 query FASTQ paths by processing tool.
workflow/​rules/​bwamem2.smk	Parameterize bwa-mem2 read FASTQ paths by processing tool.
workflow/​rules/​bowtie2.smk	Parameterize bowtie2 read FASTQ paths by processing tool.
workflow/​rules/​common.smk	Update MultiQC inputs for processing JSONs; add fastplong/minimap2 paired-end guardrails.
workflow/​rules/​mapping_stats.smk	Read plotCoverage extra args from config instead of hardcoding.
config/​schemas/​config.schema.yml	Add schema default for deeptools_plotcoverage.extra.
config/​config.yml	Set default deeptools_plotcoverage.extra in example config.
.test/​config/​config.yml	Mirror the default deeptools_plotcoverage.extra in test config.

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[rabioinf]

see my comment

[rabioinf]

looks good now