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Building Workflows
A workflow is a set of nodes on a canvas, connected from outputs to inputs. N-WAVE writes the Nextflow script from it. What each node does is in the Node reference.
On the home page:
- New Workflow offers an Empty workflow, the QC of FASTQ files template (FastQC on two test samples and a MultiQC report), or an editable copy of a built-in demo.
-
Import Workflow reads a Nextflow script (
.nf, pasted or from a file), a project zip or a project folder and draws it on the canvas; warnings show above the canvas (Importing workflows). - On a workflow card: Edit (name and description), Duplicate and Delete.
The three built-in demos are read-only. The first change you make asks whether to Make a copy: the copy opens with your change, and the demo stays as it is. Just look keeps it unchanged.
Workflows save automatically a couple of seconds after each change (Save Workflow in the bottom bar saves at once).
- + (Add node, top right) lists the nodes by kind, with a search. From there you also open the nf-core Library, the Custom process editor and Node packs.
- Double-click a node to open its panel. Its tabs: Settings, Code (the Nextflow it adds) and Results (what it produced in the last run).
- Delete a node with its panel's delete button, the Delete key, or by dragging it onto the bin in the bottom-right corner. Hover a connection and click × to remove it.
Node colors show their kind: inputs light blue, nf-core steps green, other steps grey (the legend is on the home page and on the Help page, which the canvas's ? button opens).
- Fit view (the first button at the bottom left) zooms to fit the whole workflow; the buttons next to it zoom in and out.
- Minimap: a small map of the whole canvas sits at the bottom left, above the zoom buttons, colored like the legend (inputs, nf-core steps, other steps). During and after a run it colors the steps by what they did: running, done, failed, reused from the cache, or not run yet. Drag the map or click it to move the canvas. It can be switched off for everyone in Global Settings → Features.
-
Steps inside: an nf-core subworkflow node and a Pipeline node hold several steps, so they
are drawn as a stack of cards with a Step in bar at the bottom. Like stepping into a
function in a debugger, it opens the steps inside as a read-only graph, read from the
workflow's
main.nf(in nf-core/modules for a subworkflow, in the pipeline's repository at its version for a pipeline). Stacked steps in there have steps of their own and open in turn; the breadcrumb at the top leads back out, Escape closes it. During and after a run, each step shows what it did and how many of its tasks are done. Connections follow the channels the workflow passes from one step to the next; ones N-WAVE can't follow (built in a function, for example) are left out. - Copy into new workflow (in the steps inside of an nf-core subworkflow, and in its node's panel) makes a new, editable workflow from the subworkflow's steps, to swap a tool, add a step or leave one out. The original node stays as it is (Copying a subworkflow).
- Zoom to the failing step appears next to them after a run failed and goes to the step that failed.
The switch in the bottom bar (All | Steps | Grouped) chooses what the canvas shows:
- All: every node, editable.
- Steps: channel code (channel operator nodes, and code kept from an import) is hidden, and each step connects straight to the steps its data reaches through it (dotted lines). Large imported workflows read as their steps this way. This view can't be edited: editing a node's settings, or any other change, goes back to All.
- Grouped (when the workflow has groups): each group is one box with its steps listed, connected to the rest. Open (or a double-click) goes back to All, zoomed to the group's steps. This view can't be edited either.
Connected in code (orange dashed lines): code in a node can call a step or read another
node's output that the canvas doesn't connect to it, for example an imported
if (params.trim) { TRIM(ch_reads) }. N-WAVE finds these in the code it writes for the
canvas, draws them dashed, and says so in the workflow check (a warning on the node whose code
makes them). They work without a server, in the browser demo too, and follow the
Connection hints switch (Global Settings → Features).
Steps that belong together (a quality check and its report, an alignment with its sorting and statistics) can be grouped into a subworkflow. Each step keeps its node and its settings; the group changes how the code is written and adds a way to see the workflow:
- Select the steps (click one, then Ctrl+click, or ⌘+click on a Mac, the others) and click Group into subworkflow… above the canvas. Or take a suggestion of the analysis.
- Name it. The name is the subworkflow's in the code (
Read QC→READ_QC); it can't be a step's name or another group's. - On the canvas, a frame shows the group's steps, with Rename and Ungroup (the steps on their own again). Grouped in the bottom bar shows each group as one box.
In the code, the group is a named workflow the workflow calls: what its steps read from the
other steps becomes its inputs (take:), what the other steps read from it its outputs
(emit:). It runs as before; Nextflow names its tasks READ_QC:FASTQC, and N-WAVE shows them
on their steps as usual.
workflow READ_QC {
take:
ch_samplesheet
main:
FASTQC_RAW_READS(ch_samplesheet)
TRIM_GALORE(ch_samplesheet)
emit:
reads = TRIM_GALORE.out.reads
zip = FASTQC_RAW_READS.out.zip
}
workflow {
…
READ_QC(ch_samplesheet)
STAR_ALIGN(READ_QC.out.reads, …)
}- Only steps can be grouped: inputs, outputs, Parameters and notes stay outside.
- Data can't leave a group and come back into it through a step outside: add that step to the group, or leave out the steps after it. The workflow check says when that's the case.
- Channel code inside a group that names a channel outside it by name (not through a connection) can't see that channel in the subworkflow; connect it instead.
- Importing a script or project N-WAVE wrote gives the groups back. A subworkflow written by hand imports as one step that keeps its code.
Drag from an output (the dots on a node's right) to an input (on the left).
-
Hover a node to see what each port carries (for example
*.{bam}) and whether it takes one connection or many. - While you drag, inputs that fit are ringed green and inputs that don't are amber.
- A connection that doesn't fit is still made, but drawn dashed amber with a warning mark. Click the mark to see what the input expects and how to fix it.
- Most inputs take one connection. To bring several together, connect them to a Merge node or a Channel Operator first. Inputs that gather files (a taller handle, such as Merge's input or MultiQC's) take any number.
- Loops are refused, as is connecting a node to itself.
The button next to Run checks the workflow while you build it and shows how many problems it found. Click it for the list; Show moves the canvas to the node, which also carries a red (problem) or yellow (warning) mark.
- Problems stop the run, for example a required input that isn't connected, a File Input without a file, samplesheet errors, nf-core components that aren't installed, or a server without Docker.
- Warnings don't, for example unconnected nodes or a run that asks for more than the server allows.
Check again asks the server again, for example after starting Docker.
The undo and redo buttons are next to the zoom controls. Press ? for all shortcuts:
| Keys (⌘ on macOS) | Action |
|---|---|
| Ctrl+Z / Ctrl+Shift+Z or Ctrl+Y | Undo / redo |
| Ctrl+C, Ctrl+X, Ctrl+V | Copy, cut, paste the selected nodes (also into another workflow) |
| Ctrl+D | Duplicate the selected nodes |
| Delete or Backspace | Delete the selection |
| Ctrl+A, Shift+click | Select all, select several |
| F | Fit the workflow into view |
| Ctrl+S, Ctrl+Enter | Save, run |
Shortcuts don't fire while you type in a field. While a run goes, the workflow is locked (an amber frame says so) until the run ends.
The workflow saves itself two seconds after a change (or press the save button). A save never overwrites a newer version saved in another tab: if the workflow was changed elsewhere since you opened it, N-WAVE asks what to keep. You can load the saved version, keep yours as a copy, or replace the saved version with yours. Changing or deleting a custom node also updates the saved workflows that use it; a tab open on one of them shows that version when you come back to it, or asks the same question if it has unsaved changes.
Download Workflow saves the script, Export Project a runnable project. See Exporting projects.
- Running workflows
- Custom nodes, for steps of your own
- The Help page in N-WAVE (its glossary), for terms such as channel, tuple or meta