Single-cell & spatiallatest-release

rangeland

nf-core/rangeland

Long-term vegetation trend analysis pipeline for rangeland systems using satellite imagery.

version1.0.07c5cb9593bJan 17, 2025 Upstream Usage docs

Key tools

FORCEMultiQC

Parameters

Groups

nf-core modules

Samplesheet cols

Run it

nfclaw

nfclaw run rangeland --input <input> --outdir results --dem <dem> --wvdb <wvdb> --data-cube <data_cube> --aoi <aoi> --endmember <endmember> -profile docker

raw nextflow

nextflow run pipelines/rangeland/upstream -profile docker --input <input> --outdir results --dem <dem> --wvdb <wvdb> --data_cube <data_cube> --aoi <aoi> --endmember <endmember>

demo · bundled test profile

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

Inputs

This release publishes no samplesheet schema for --input, so nfclaw does not pre-check its contents. The parameter reads: Root directory or tarball of all satellite imagery. Configure the other inputs via parameters (see reference.md).

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 rangeland --input <input> --outdir results --dem <dem> --wvdb <wvdb> --data-cube <data_cube> --aoi <aoi> --endmember <endmember> -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 = '!>=24.04.2'.

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

bash

nfclaw run rangeland ... --nxf-ver 24.04.2

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

Demo

bash

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

Required parameters

--inputstring (file or directory path)

Root directory or tarball of all satellite imagery.

--demstring (file or directory path)

Digital elevation model.

--wvdbstring (file or directory path)

Water vapor dataset.

--data-cubestring (file path)

Datacube definition.

Constraint · matches ^\S+\.prj$

--aoistring (file path)

Area of interest.

Constraint · matches ^\S+\.(gpkg|shp)$

--endmemberstring (file path)

Endmember definition.

Constraint · matches ^\S+\.txt$

--outdirstring (directory path)

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

Parameter explorer

40 parameters · 7 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

22 parameters · 18 hidden

Generic options1

Custom MultiQC yaml file containing HTML including a methods description.

Higher Level Processing Modification2

Select which bands and indexes should be considered in time series analyses.

Should the full time series stack be returned.

Input Output options9

Area of interest.

Datacube definition.

Digital elevation model.

Email address for completion summary.

Endmember definition.

Root directory or tarball of all satellite imagery.

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.

Water vapor dataset.

Remote Sensing Image options4

Last day of interest.

Spatial resolution applied in analyses.

Satellites for which data should be incorporated into higher level processing.

First day of interest.

Visualization2

Whether mosaic visualization should be returned.

Whether pyramid visualization should be returned.

Workflow Configuration4

Batch size of tiles considered for merging.

Publish pipeline outputs.

Whether analysis ready data should be published to the output directory.

Whether the results of time series analyses should be published to the output directory.

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/rangeland/blob/1.0.0/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.