fix: release please workflow #10
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feat: complete minimal workflow as template
feat: updated github actions workflow
fix: update release-please GH workflow
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Caution Review failedThe pull request is closed. WalkthroughThis update enhances GitHub workflows, configuration files, documentation, and the Snakemake pipeline. In GitHub Actions, workflow names, permissions, triggers, and dependency versions have been updated. New configuration and schema files for genomic data processing and sample sheet validation have been added. The Snakemake workflow now loads a configuration file, includes external rule files, and features new logging hooks and a default target. Additionally, several Conda environment definitions and a Python script for genome retrieval have been introduced to support new rules covering genome retrieval, read simulation, quality control, adapter trimming, and MultiQC report aggregation. Changes
Sequence Diagram(s)sequenceDiagram
participant SF as Snakefile
participant CG as get_genome.py
participant SR as simulate_reads
participant FQ as fastqc
participant CA as cutadapt
participant MQ as multiqc
Note over SF: Workflow Starts (onstart)
SF->>CG: Trigger get_genome rule
CG-->>SF: Return genome (FASTA, GFF)
SF->>SR: Trigger simulate_reads rule
SR-->>SF: Output simulated FASTQ files
SF->>FQ: Trigger fastqc rule
FQ-->>SF: Return quality report
SF->>CA: Trigger cutadapt rule
CA-->>SF: Return trimmed FASTQ files
SF->>MQ: Trigger multiqc rule
MQ-->>SF: Return aggregated MultiQC report
Note over SF: Workflow Ends (onsuccess)
Poem
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