readsimulator
nf-core/readsimulator
A workflow to simulate reads
Key tools
Run it
nfclaw run readsimulator --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/readsimulator/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run readsimulator --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sample | string | yes | matches ^\S+$ | |
seed | integer | yes |
--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):
sample,seedFrom 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).
Reference genome
No reference genome is set by default: supply your own reference. A genome name alone does not specify where reference files come from. Confirm the selected reference's paths and source in the pinned upstream/nextflow.config and upstream/conf/ before running. To supply your own reference, use e.g. --fasta; the reference_genome_options group in reference.md lists every reference option. Set --igenomes-ignore true to disable the lookup entirely.
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 readsimulator --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 = '!>=23.04.0'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run readsimulator ... --nxf-ver 23.04.0--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.
Nextflow 23.04.0 predates process.resourceLimits (24.04.0), so --limit-* cannot be combined with this pin — nfclaw refuses it rather than run without the ceiling; cap resources with the release's own --max-cpus, --max-memory, --max-time instead.
Demo
nfclaw run readsimulator --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.
sample,seed| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string | required | matches ^\S+$ |
seed | integer | required | — |
Required parameters
--inputstring (file path)Path to comma-separated file containing information about the samples in the experiment.
Constraint · matches ^\S+\.csv$
--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
76 parameters · 10 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.
52 parameters · 24 hidden
Amplicon options6
Maximum number of errors allowed in CRABS insilicoPCR primer sequences
Forward primer to use with crabs_insilicopcr.
Number of reads to be simulated per amplicon.
Length of reads to be simulated.
Reverse primer to use with crabs_insilicopcr.
Sequencing system of reads to be simulated.
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.
Metagenome options9
Abundance distribution.
Path to tab-separated file containing abundance distribution.
Coverage distribution.
Path to tab-separated file containing coverage information.
Use this option to prevent simulating reads that have abnormal GC content.
Format of FASTA file used to generate reads
Can be 'kde', or 'basic'.
Can be 'HiSeq', 'NovaSeq', or 'MiSeq'.
Number of reads to generate.
Reference Genome options6
Path to reference FASTA file.
Name of iGenomes reference.
Path to text file containing accession ids (one accession per row).
The NCBI taxonomic groups to download. Options include 'all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', and 'viral'. A comma-separated list is also valid (e.g., 'bacteria,viral').
The NCBI section to download. 'refseq' or 'genbank'.
Path to text file containing taxids (one taxid per row).
Simulation options4
Option to simulate amplicon sequencing reads.
Option to simulate metagenomic sequencing reads.
Option to simulate target capture sequencing reads.
Option to simulate wholegenomic sequencing reads.
Target Capture options13
Path to bait/probe file. Can be a fasta file or a bed file.
Name of supported probe. Mandatory if not using --probes parameter.
Median of fragment size at shearing.
Shape parameter of the fragment size distribution.
Illumina: read length.
Illumina: Sequencing mode.
Simulate 'illumina' or 'pacbio' reads.
Number of fragments.
PacBio: Average (polymerase) read length.
Median of fragment size distribution.
Shape parameter of the fragment size distribution.
Median of target fragment size (the fragment size of the data). If specified, will override '--fmedian' and '--smedian'. Othersise will be estimated.
Shape parameter of the effective fragment size distribution.
Wholegenome options9
The base error rate.
The probability that an indel is extended.
The fraction of indels.
The rate of mutations.
The number of read pairs.
The outer distance between the two ends.
The length of the first reads.
The length of the second reads.
The standard deviation.
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/readsimulator/blob/1.0.1/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.