Merge new zsh-dependent config revamp into master

[agillen]

No description provided.

[Copilot]

Pull request overview

Revamps the pipeline configuration to be zsh-based and to use hierarchical YAML configuration for per-sample/per-chemistry/per-platform settings.

Changes:

• Switches the workflow shell to zsh and adds hierarchical config lookup via SAMPLES + chemistry.yaml.
• Refactors cutadapt/STAR rules to pull parameters from config instead of TSV/JSON-driven logic.
• Removes legacy sample/chemistry artifacts (sample_fastqs.tsv, chemistry.json, generator script) and updates docs/developer guide.

Reviewed changes

Copilot reviewed 13 out of 14 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
scraps_conda.yml	Updates environment deps (STAR constraint loosening; adds zsh).
sample_fastqs.tsv	Removes legacy sample sheet.
Snakefile	Switches to zsh and adds hierarchical _get_config() + new rule-all output assembly.
config.yaml	Introduces DEFAULTS + SAMPLES structure replacing TSV-driven sample config.
chemistry.yaml	Adds new hierarchical chemistry/platform parameter definitions.
rules/cutadapt_star.snake	Refactors trimming/alignment params to come from _get_config()/chemistry.yaml.
rules/count.snake	Updates inputs to match new alignment outputs and adds pre-featureCounts filtering.
rules/qc.snake	Adjusts QC inputs to use SAMPLES keys.
inst/scripts/cut_paste_fastq.py	Adds optional length-based trimming support for stitched FASTQ reconstruction.
README.md	Updates setup/config documentation to match new YAML-based configuration.
AGENTS.md	Adds developer guide and conventions for working in this repo.
chemistry_to_json.py	Removes obsolete JSON generator.
chemistry.json	Removes obsolete chemistry JSON.

Comments suppressed due to low confidence (1)

rules/count.snake:45

• assign_sites_R1 writes an intermediate filtered BAM to {params.temp} but never removes it. This will leave large files behind (unlike assign_sites_paired, which cleans up). Add cleanup for {params.temp} once it's no longer needed (and consider declaring it as a temp() output instead of a params path).

    samtools sort \
    {params.out_bam} \
    -o {output.bam}

    samtools index {output.bam}
    rm -rf {params.out_bam}
    """

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[Copilot]

There are leftover debug prints (print(length1)) in both paste_fastq and main(). This will add noisy stdout in Snakemake logs and can interfere with callers that expect the script to be quiet on success. Remove these prints or gate them behind an explicit --verbose flag.

[Copilot]

In the paired trimming branch, [ -z {params.bc_cut} ] is unquoted. When bc_cut is empty this expands to [ with a missing argument, causing a shell error; when it contains special chars it can also undergo word-splitting. Quote the substitution (e.g. "{params.bc_cut}") or otherwise ensure a safe test expression.

[agillen]

@copilot open a new pull request to apply changes based on this feedback

[Copilot]

@agillen I've opened a new pull request, #83, to work on those changes. Once the pull request is ready, I'll request review from you.