phyloplace
nf-core/phyloplace
Performs phylogenetic placement with EPA-NG
Key tools
Run it
nfclaw run phyloplace --outdir results -profile dockernextflow run pipelines/phyloplace/upstream -profile docker --outdir resultsnfclaw run phyloplace --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:
nfclaw run phyloplace --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 = '!>=26.04.0'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run phyloplace ... --nxf-ver 26.04.0--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run phyloplace --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.
Parameter explorer
37 parameters · 3 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.
19 parameters · 18 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 options15
Method used to align query sequences with.
Email address for completion summary.
HMM file. If provided, will be used to align both the reference and query sequences.
Name of analysis
Evolutionary model to use for placement, e.g. 'LG'.
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.
Path to comma-separated file containing information about phylogenetic placements to perform.
Path to comma-separated file containing information about phylogenetic searches to perform.
Fasta file with query sequences
Newick file with the reference phylogeny.
File with reference sequences. Any format supported by HMMER tools.
Save the per-domain hit table (--domtblout) from hmmsearch.
Fasta file with sequences to be searched with HMM profiles.
Tab-separated file with taxonomy assignments of reference sequences.
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/phyloplace/blob/2.3.0/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.