Testing

Test profile wiring

conf/test.config defines a minimal smoke dataset (data/reads/illumina_reads_40.fasta.gz) and writes to results_test/.

Recommended checks

make lint

nextflow run . -profile test,local

bash tests/smoke/check_outputs.sh results_test

CI strategy (minimal)

• Lint Perl + Python helper scripts.
• Run a smoke workflow (test,local) on bundled data.
• Assert expected output artifacts exist.