metapep
nf-core/metapep
From metagenomes to peptides
Key tools
Run it
nfclaw run metapep --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/metapep/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run metapep --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
condition | string | yes | matches ^\S+$ | |
type | string | yes | bins, assembly, taxa | |
microbiome_path | string (file path) | yes | matches ^\S+$ | |
alleles | string | yes | ||
weights_path | string (file path) | no | matches ^\S+$ |
--input must match ^\S+\.csv$.
The samplesheet is a CSV with this header (the columns the schema requires); fill each value per the table above and reference.md (no example value is invented here):
condition,type,microbiome_path,allelesAny of the optional columns above may be appended to the header when your data needs them: weights_path.
From data files. nfclaw cannot generate this samplesheet: the samplesheet declares no file type nfclaw could match files against (no column's pattern names a file extension).
Secrets
This release reads Nextflow secrets: NCBI_EMAIL (in modules/local/download_proteins.nf); NCBI_KEY (in modules/local/download_proteins.nf). Set each one a run needs with nextflow secrets set NAME VALUE before launching; a secret that is not set reaches its tasks as an empty value (Nextflow warns that the variable evaluates to an empty value), and a task that needs it then fails. Secrets are not written to nfclaw's provenance.
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:
nfclaw run metapep --input samplesheet.csv --outdir results -profile docker \ --limit-cpus 4 --limit-memory 15.GBnfclaw 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:
nfclaw run metapep ... --nxf-ver 24.04.2--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run metapep --demo --outdir results # adds the upstream test profile (-profile test,docker)Samplesheet
A CSV with this header (the columns the schema requires). Fill each value per the constraints below; optional columns from the table may be appended.
condition,type,microbiome_path,alleles| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
condition | string | required | matches ^\S+$ |
type | string | required | binsassemblytaxa |
microbiome_path | string (file path) | required | matches ^\S+$ |
alleles | string | required | — |
weights_path | string (file path) | optional | matches ^\S+$ |
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.
Parameter explorer
38 parameters · 4 groupsEvery 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.
14 parameters · 24 hidden
Generic options1
Custom MultiQC yaml file containing HTML including a methods description.
Input Output options4
Email address for completion summary.
Path to comma-separated file containing information about the samples in the experiment.
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.
Pipeline options9
Maximum chunk size (#epitope predictions) for processing of downstream visualisations.
Do not display mean comparison p-values in boxplots.
Maximum length of produced peptides.
Maximum number of tasks submitted by PREDICT_EPITOPES process
Minimum length of produced peptides.
Epitope prediction method to use
Maximum chunk size (#peptides) for epitope prediction jobs.
Prodigal mode, 'meta' or 'single'.
Display supported alleles of all prediction methods and exit.
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/metapep/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.