clusterprofiler plugin

This plugin exposes Bioconductor clusterProfiler enrichment nodes as an Autonomics File-to-File container family.

Nodes

clusterprofiler_ora

clusterprofiler_ora reads:

1. a TSV with a unique gene-identifier column (default gene);
2. a GMT pathway collection with at least one gene after each pathway name.

It calls clusterProfiler::enricher() and writes:

• clusterprofiler_ora.tsv
• clusterprofiler_ora.json

The TSV retains the stable upstream result columns. The JSON report records parameters, input sizes, result count, and the installed clusterProfiler version. A zero-row enrichment result is valid.

clusterprofiler_gsea

Reads:

1. a TSV rank table with unique gene identifiers and finite numeric score values (input order may be unsorted);
2. a GMT pathway collection.

It sorts scores decreasingly, calls clusterProfiler::GSEA(), and writes:

• clusterprofiler_gsea.tsv
• clusterprofiler_gsea.json

The TSV retains the stable upstream result columns. The JSON report records parameters, input and eligible-set sizes, result count, and the installed clusterProfiler version. Pathways with no ranked genes are not eligible and a zero-row enrichment result is valid.

Both nodes use caller-supplied GMT collections and do not query online GO or KEGG services.

Local development

podman build --format docker \
  -t localhost/autonomics/clusterprofiler:0.1.0 .
CLUSTERPROFILER_RUNNER=container ./test_clusterprofiler_ora.sh
CLUSTERPROFILER_RUNNER=container ./test_clusterprofiler_gsea.sh

For a host R installation containing clusterProfiler, data.table, and jsonlite, use:

CLUSTERPROFILER_RUNNER=local ./test_clusterprofiler_ora.sh
CLUSTERPROFILER_RUNNER=local ./test_clusterprofiler_gsea.sh

The manifest references the digest-pinned image published at ghcr.io/auto-nomics/autonomics/clusterprofiler.

Current local build:

• clusterProfiler 4.16.0
• data.table 1.18.6.1
• jsonlite 2.0.0

Security

The nodes keep the hardened defaults: isolated networking and a read-only image root filesystem. Explicit resource limits are 2 CPUs, 8 GiB memory, 512 PIDs, and 1 GiB shared memory. Only /work, /tmp, and /dev/shm are writable at runtime.