feat: add apptainer.def + document the published SIF on Docker Hub - #3
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Adds a native Apptainer definition (mirrors the Dockerfile: miniforge3 base, the 8 per-rule conda envs pre-baked at /opt/wf-conda, rootless-apt fix) so the image builds on HPC without Docker. README: Docker Hub pulls badge and an Apptainer path that pulls the published SIF via ORAS (oras://docker.io/gynecoloji/chipseq-pipeline:latest) or builds locally from the definition; notes that the Docker Hub tag is a SIF (not `docker pull`-able). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
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Summary
Adds native Apptainer support and documents the SIF published to Docker Hub.
Changes
apptainer.def(new) — mirrors the Dockerfile: miniforge3 base, rootless-aptfix,
snakemake-minimal=9.3.2driver, all 8 per-rule conda envs pre-baked at/opt/wf-conda. Builds on HPC without Docker:apptainer build --fakeroot chipseq-pipeline.sif apptainer.def.gynecoloji/chipseq-pipeline) and anApptainer path that pulls the published SIF via ORAS
(
apptainer pull … oras://docker.io/gynecoloji/chipseq-pipeline:latest) or buildslocally. Notes the Docker Hub tag is a SIF (ORAS artifact), so
docker pullwon't work on it — the Docker path stays a local
docker build.Verified
Built and smoke-tested the SIF: 8 envs baked; bowtie2, MACS2, IDR, bedtools,
deepTools (
computeMatrix), HOMER (findMotifsGenome.pl), and ChIPseeker 1.46.1all load