Inputs and outputs

Inputs

Mode A: glob input mode

• Reads from --input glob (default: data/reads/*.fasta.gz)
• Shared annotation defaults from --annotation_dir/override params

Mode B: samplesheet mode

CSV columns:

sample,reads,chromosome,gff,tss,cpg,repeatmasker

Each row defines one processing unit with explicit chromosome/annotation mapping.

Outputs

• results/matched/*.matched
• results/annotated/*.annotated.tsv
• results/all_samples.annotated.tsv
• results/summary_counts.txt
• results/gene_counts.png
• results/gene_cpg_gc.png
• results/tss_distance.png
• results/tss_type.png
• results/pipeline_info/{trace,report,timeline,dag} (or --tracedir override)