Run a Guided Workflow
Let a step-by-step workflow run a standard analysis and ask you at each key decision.
For standard analyses such as scRNA-seq QC and clustering, flow cytometry gating or microscopy segmentation, a guided workflow runs Drylab's tested steps. It pauses whenever a choice should be yours, with the evidence in front of you. In Drylab these are called structured workflows.
When to use it
- You have raw single-cell counts and want QC, doublet removal and clustering done the standard way, with the cutoffs chosen by you.
- You're gating flow cytometry data or segmenting microscopy images and want to check each gate or mask yourself.
- You want the same steps every time, across samples, students or projects.
- You need to report how each step was done, with the values you chose.
Prompt examples
Type @w and pick the workflow; @<workflow name> in the examples stands for its chip.
scRNA-seq QC and clustering:
@scRNA QC + Clustering on @pbmc_10k.h5 (human, mitochondrial genes start with MT-). Start from a minimum of 200 genes per cell and at most 10% mitochondrial reads, and try resolutions 0.4 to 1.2.Cell-type annotation after clustering:
@scRNA Cell-Type Annotation on @pbmc_clustered.h5ad. Use these markers: T cells CD3E, B cells MS4A1, NK cells NKG7, monocytes CD14 and LYZ, platelets PPBP.Flow cytometry:
@Flow Cytometry Analysis on the FCS files in @fcs_run_01. The controls are the FMO files, and the panel is in @panel.csv.Microscopy:
@Microscopy Segmentation (with human feedback) on @nuclei_dapi.tif, segment the nuclei and drop objects smaller than 30 pixels.Steps
- Before you start, open Analysis settings (the gear next to the send button) and set Step review to Every step the first time you run a workflow on a new dataset. See Analysis settings.
- In the chatbox, type
@w(with a space) and a keyword, for example@w scrna. The Workflows tab lists the matching workflows and how many steps each has.@w scrnalists scRNA Cell-Type Annotation, scRNA QC + Clustering and Spatial Domain Detection & Annotation. - Hover a workflow to open the Resource Preview. Read the numbered Steps & Artifacts: the tag next to a step, such as Single Choice, Image Choice, Gating Tree or Custom, shows how Drylab will ask you. The legend marks each step as Step, Review or Decision.
- Click the workflow, then Click to use resource, or press Enter. It becomes a chip in your message.
- Mention your data in the same message (type
@and the file name) and add what you already know: organism, controls, metadata columns, thresholds. - Send it, review the plan and click Approve Plan.
- When a step needs your choice, Drylab pauses with a Decision needed card. Check the evidence, change the selection if you want to, and click Continue.
- With Step review on, Drylab also pauses after steps. Click Approve & continue, or Request changes and describe what to redo.
At the end, Drylab summarizes the results in the chat, and the notebook holds every step with the values you chose. See Save Results to the Same Workspace.
The tag next to each step in the preview shows how Drylab will ask you: pick an option, click the best image, drag a threshold, edit a table or adjust gates. How to answer each card is explained in Plans and Questions.
Tips
- Use Every step on new data. Relax Step review to Key steps on a rerun, once you trust the thresholds.
- Report the values you chose. At the end, ask "list every decision and the value I picked". It's the start of your methods paragraph.
- Chain workflows. After scRNA QC + Clustering, mention its clustered object with scRNA Cell-Type Annotation in the same chat or a new one. See Continue from an Earlier Result.