Input / Output Nodes
I/O nodes bring data into a workflow and take results out. They are the entry and exit points of every graph.
Input nodes
FASTQ Input
Loads single- or paired-end sequencing reads.
| Parameter | Type | Description |
|---|---|---|
r1 | File | Read 1 (.fastq / .fastq.gz) |
r2 | File | Read 2 (optional, for paired-end) |
sample | String | Sample name used in read groups |
Outputs: reads: FASTQ
Reference Input (FASTA)
Provides a reference genome or transcriptome.
| Parameter | Type | Description |
|---|---|---|
fasta | File | Reference sequence (.fa / .fasta) |
buildIndex | Bool | Build aligner indices on load |
Outputs: reference: FASTA
SRA / ENA Download
Fetches public reads by accession (e.g. SRR…, ERR…) directly into the run.
Outputs: reads: FASTQ
Generic File / Directory Input
Loads an arbitrary file or folder as a File / Directory for nodes that accept
generic inputs.
Output nodes
VCF / BAM / FASTA Output
Marks an artifact as a workflow result. Output nodes make their upstream data downloadable from the run detail page and (in the cloud) persist it to versioned object storage.
| Parameter | Type | Description |
|---|---|---|
filename | String | Name for the exported artifact |
persist | Bool | Keep beyond the run’s TTL (cloud) |
Report Output
Surfaces an HTML/PDF report (FastQC, MultiQC, QUAST) so it renders inline in the run view.
Tips
- Connecting a node to an Output node is what makes its result downloadable — intermediate results are cached but not exported unless you ask for them.
- Use SRA / ENA Download to build fully self-contained, shareable example workflows that need no local files.