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nf-sra_screen 0.4.0 software provenance

Version selection was completed on 6 August 2026. Registry publication and digest verification were completed on 7 August 2026.

Scope

This record covers direct pipeline tools, workflow runtimes, custom-image bases, and explicitly installed scientific libraries. Transitive packages are captured by immutable image digests and the custom-image inventories. Database/reference assets, including the existing Sandpiper and GTDB filenames, are unchanged and deferred to the future db_prep work.

  • software.tsv is the direct-version source of truth.
  • images.tsv maps every configured process image to its digest, architecture, processes, direct versions, build date, and inventory.
  • packages/ contains conda list --explicit and pip freeze --all output exported from each published custom-image digest.

Custom builds

All nine custom images were cross-built and loaded locally as linux/amd64 images with Docker Buildx. Their common base is condaforge/miniforge3:26.3.2-3@sha256:95195a50e20f7929a31a68ea407cefe117423258639efb6b66f0518e4b86f8ee, the registry's linux/amd64 platform digest. New versioned tags were used; no existing tag was overwritten.

The custom Myloasm image combines Myloasm 0.6.0 with mylotools 2.1.0 so final_contig_graph.gfa can be reconciled with the polished, filtered assembly before the pipeline publishes assembly.gfa.

COMEBin retains PyTorch 1.13.1/CUDA 11.7. VAMB and LorBin GPU retain PyTorch 2.6.0/CUDA 12.4. LorBin uses upstream commit e35c65b3a97fe225b04dc0beaddb85fcc4a1af7c. These compatibility stacks were not loosened while moving from Mambaforge to Miniforge.

Validation

Each custom image passed its Dockerfile build assertions and local version/import/CLI checks before publication. After publication, verify_custom_images.sh pulled all nine by their tag-and-digest reference and repeated the checks. The mapping image also passed a tiny Bowtie2/SAMtools/minimap2 read-to-reference smoke test. Published manifest digests were independently resolved with Docker Buildx and match images.tsv.

test_container_provenance.py rejects mutable or malformed refs, missing digests, undocumented process images, direct-version mismatches, missing custom inventories, and workflow-runtime version drift.

GPU validation is limited to image build, imports, package consistency, and PyTorch CUDA build metadata. No GPU hardware execution or numerical validation is claimed. A full reference-dependent scientific workflow was not run; database preparation and corresponding end-to-end validation remain outstanding for db_prep.