Single-cell & spatiallatest-release

mcmicro

nf-core/mcmicro

Whole-slide multiplexed microscopy image analysis

version2.0.0f440000157Jul 1, 2026 Upstream Usage docs

Key tools

ASHLARBacksubBaSiCPyBioformatsCellposeCoreographMCQuantMesmerMultiQCSciMap

Parameters

Groups

nf-core modules

Samplesheet cols

Run it

nfclaw

nfclaw run mcmicro --outdir results --marker-sheet <marker_sheet> -profile docker

raw nextflow

nextflow run pipelines/mcmicro/upstream -profile docker --outdir results --marker_sheet <marker_sheet>

demo · bundled test profile

nfclaw run mcmicro --demo --outdir results   # adds the upstream test profile (-profile test,docker)

Inputs

This pipeline does not use a samplesheet; configure inputs via parameters.

Resources

Resource requests follow the pipeline's configs and selected profiles. nf-core's resource labels often assume a server — a single step can request far more memory than a workstation has, and retry rules can increase requests. If a run fails with Process requirement exceeds available memory (or CPUs), cap every request, and every retry, at what this machine actually has:

bash

nfclaw run mcmicro --outdir results --marker-sheet <marker_sheet> -profile docker \
  --limit-cpus 4 --limit-memory 15.GB

nfclaw turns those into Nextflow's process.resourceLimits and passes them as a -c config — the mechanism nf-core prescribes for exactly this (docs). Set them to the machine's real capacity. --limit-time DURATION also caps how long any one task may run: a task that needs longer is stopped, and so is every retry, so set it only as a deliberate ceiling, never as a guess at how long the analysis takes. The generated config is kept in <outdir>/provenance/, so commands.sh replays the run under the same ceiling.

Nextflow engine

This release declares nextflowVersion = '!>=25.04.0'.

To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:

bash

nfclaw run mcmicro ... --nxf-ver 25.04.0

--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.

Demo

bash

nfclaw run mcmicro --demo --outdir results   # adds the upstream test profile (-profile test,docker)

Required parameters

--outdirstring (directory path)

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

--marker-sheetstring (file path)

Path to comma-separated file containing information about the markers

Constraint · matches ^\S+\.csv$

Parameter explorer

35 parameters · 3 groups

Every parameter from the pinned nextflow_schema.json. nfclaw checks explicit values before launch; complex rules use the pinned pipeline's runtime validation. Search, filter by group, and expand any parameter for its default, allowed values and constraints.

Groups

nextflow_schema.json

16 parameters · 19 hidden

Generic options4

Display the help message.

Display the full detailed help message.

Custom MultiQC yaml file containing HTML including a methods description.

Display hidden parameters in the help message (only works when --help or --help_full are provided).

Input Output options12

boolean to flag whether or not to apply background subtraction

optional model file for cellpose segmentation

Email address for completion summary.

input that defines type of illumination correction to be performed

Path to comma-separated file containing information about the samples in the experiment.

Path to comma-separated file containing information about the markers

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Run the pipeline in prelude mode. Extracts metadata writes MultiQC table and exits.

comma separated list of segmentation modules to run. options are ['mccellpose','cellpose','mesmer']

If the sample is a tissue microarray (TMA), set this to 'true' to generate a separate output for each tissue core for pipeline steps beginning with cell segmentation. This also tends to speed up processing and reduce RAM usage.

Outputs

Results land in --outdir; the files and directory layout depend on the selected workflow, parameters and publication settings. Run metadata is normally placed in <outdir>/pipeline_info/ (execution report, software versions), when those outputs are enabled. The pinned tree includes MultiQC support; a report is produced only when its workflow step runs. nfclaw run also writes <outdir>/provenance/ with the exact params file and the run log, <outdir>/provenance/logs/run.log — the whole launch, whose last line states the outcome (Nextflow's own log is <outdir>/.nextflow.log); unless --no-provenance it adds a run manifest (pinned version, commit and exact command), input/output SHA-256 checksums, and a replayable commands.sh. The exact output files and directory layout for this release are documented upstream: github.com/nf-core/mcmicro/blob/2.0.0/docs/output.md Check a run — in the foreground or the background — with nfclaw status <outdir>: success, still running, how it ended (with the error), or stopped without an outcome; exit 0 success, 3 running, 1 otherwise.