plasmodiumdrugres
nf-core/plasmodiumdrugres
This pipeline takes PMO format and provides key metrics on supplied markers applicable to drug resistance
Key tools
Run it
nfclaw run plasmodiumdrugres --outdir results --loci-of-interest-bed <loci_of_interest_bed> -profile dockernextflow run pipelines/plasmodiumdrugres/upstream -profile docker --outdir results --loci_of_interest_bed <loci_of_interest_bed>nfclaw run plasmodiumdrugres --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: Path to input samplesheet (unused; kept for nf-core template lint compatibility). 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:
nfclaw run plasmodiumdrugres --outdir results --loci-of-interest-bed <loci_of_interest_bed> -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 = '!>=25.10.4'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run plasmodiumdrugres ... --nxf-ver 25.10.4--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Demo
nfclaw run plasmodiumdrugres --demo --outdir results # adds the upstream test profile (-profile test,docker)Required parameters
--loci-of-interest-bedstring (file path)Path to BED file containing individual loci of interest.
Constraint · matches ^\S+\.bed$
Parameter explorer
45 parameters · 5 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.
25 parameters · 20 hidden
Generic options3
Display the help message.
Display the full detailed help message.
Display hidden parameters in the help message (only works when --help or --help_full are provided).
Input Output options11
Path to tab separated file containing microhaplotypes for specimens.
Email address for completion summary.
Path to tab separated file containing groups of loci of interest. Multi-locus allele frequency estimation is skipped when this parameter is not provided.
Path to BED file containing individual loci of interest.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Path to BED file containing panel location information.
Path to json file containing metadata and microhaplotypes according to pmo format.
Comma-separated list of PMO specimen metadata field names to combine into the population label (e.g. "collection_country, collection_date"). Whitespace is ignored.
String used to join the selected pmo_population_fields when building the population label.
How to handle specimens with more than one library sample in the PMO.
Path to tab separated file containing population assignment for each specimen_name.
Method options9
Sum amino acid calls across all targets covering a locus instead of using only the target with the highest read count.
Average complexity of infection (COI) assumed for every specimen when --mlaf_method is FEM.
Method for multi-locus allele frequency estimates.
Naive MLAF method when --mlaf_method is naive.
Naive SLAF method when --slaf_method is naive.
label for population/ this individual pipeline run.
Method for single-locus allele frequency estimates.
Tool used for --slaf_method mhaps_freq.
Extra arguments supplied when translating loci of interest
Reference Genome options2
Path to FASTA file containing the full genome.
Path to FASTA file containing the reference for only the targets.
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. 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/plasmodiumdrugres/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.