Requirements on the cluster

Two live in $NEXTFLOW_DIR/bin and are invoked by absolute path: nextflow and lbzip2 (the latter only for .bz2 inputs). The rest are expected on PATH: apptainer, Slurm (sbatch/squeue/scancel/sinfo), jq, curl, aws CLI, pigz, md5sum, and zip. Bash 5.1+ (the scripts use ${var^^}, ${var,,}, and associative arrays). GNU date on the login node, for the relative-date arithmetic behind expiration (date -d "+6 months"). jq and curl are needed on the compute nodes as well as the login node, because the Wrike helpers run there too, and apptainer is needed there for AMPLISEQ's region detection, which runs vsearch from a pinned container.

Two references have to be built once before the pipelines that read them will run: scripts/build_16s_reference.sh for the ampliseq region detector, and scripts/build_host_reference.sh plus scripts/fetch_taxprofiler_db.sh for the taxprofiler pipelines.