Reproducibility: pin raw_fastq_qc env tool versions#1
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envs/raw_fastq_qc.yaml previously left fastqc/fastq-screen/bowtie2/multiqc unpinned. Pin to the same versions used across the other pipelines (fastqc 0.12.1, fastq-screen 0.15.3, bowtie2 2.5.4, multiqc 1.25) so the contamination-QC env resolves deterministically. Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
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Summary
envs/raw_fastq_qc.yamlleftfastqc,fastq-screen,bowtie2, andmultiqcunpinned, so the contamination-QC environment could resolve to different tool versions over time. Pinned to the versions already used across the other ORACLE pipelines (fastqc 0.12.1, fastq-screen 0.15.3, bowtie2 2.5.4, multiqc 1.25).This was the main remaining version-pin gap from the reproducibility audit; the scientific
scrna.yaml/r_env.yamlenvs use lower bounds intentionally to track the fast-moving scverse stack.🤖 Generated with Claude Code