genomeassembler
nf-core/genomeassembler
Assemble genomes from long ONT or pacbio HiFi reads
Key tools
Run it
nfclaw run genomeassembler --input samplesheet.csv --outdir results -profile dockernextflow run pipelines/genomeassembler/upstream -profile docker --input samplesheet.csv --outdir resultsnfclaw run genomeassembler --demo --outdir results # adds the upstream test profile (-profile test,docker)Inputs
| column | type | required | allowed values | constraints |
|---|---|---|---|---|
sample | string | yes | matches ^\S+$ | |
group | string | no | matches ^\S+$ | |
ref_fasta | string (file path) | no | ||
ref_gff | string (file path) | no | ||
use_ref | boolean | no | ||
strategy | string | no | ||
assembler | string | no | flye, hifiasm, flye_hifiasm, hifiasm_hifiasm, flye_flye, hifiasm_flye | |
assembly_scaffolding_order | string | no | ont_on_hifi, hifi_on_ont | |
genome_size | string | no | ||
flye_mode | string | no | --pacbio-raw, --pacbio-corr, --pacbio-hifi, --nano-raw, --nano-corr, --nano-hq | |
flye_args | string | no | ||
hifiasm_args | string | no | ||
assembler_ont | string | no | ||
assembler_ont_args | string | no | ||
assembler_hifi | string | no | ||
assembler_hifi_args | string | no | ||
ontreads | string (file path) | no | ||
ont_collect | boolean | no | ||
ont_adapters | string | no | ||
ont_fastplong_args | string | no | ||
hifireads | string (file path) | no | ||
hifi_adapters | string | no | ||
hifi_fastplong_args | string | no | ||
jellyfish | boolean | no | ||
jellyfish_k | integer | no | ||
jellyfish_size | string | no | ||
polish | string | no | pilon, dorado, medaka, dorado+pilon, medaka+pilon | |
polish_pilon | boolean | no | ||
polish_dorado | boolean | no | ||
polish_medaka | boolean | no | ||
medaka_model | string | no | ||
scaffold_longstitch | boolean | no | ||
scaffold_links | boolean | no | ||
scaffold_ragtag | boolean | no | ||
scaffold_hic | boolean | no | ||
hic_aligner | string | no | bwa-mem2, minimap2 | |
merqury | boolean | no | ||
qc_reads | string | no | ont, hifi | |
busco | boolean | no | ||
busco_db | string (directory path) | no | ||
busco_lineage | string | no | ||
quast | boolean | no | ||
ref_map_bam | string (file path) | no | ||
assembly | string | no | ||
assembly_map_bam | string (file path) | no | ||
csi_index_size | integer | no | ||
lift_annotations | boolean | no | ||
use_short_reads | boolean | no | ||
shortread_trim | boolean | no | ||
meryl_k | integer | no | ≥ 1 | |
shortread_F | string (file path) | no | ||
shortread_R | string (file path) | no | ||
paired | boolean | no | ||
hic_trim | boolean | no | ||
hic_F | string (file path) | no | ||
hic_R | string (file path) | no |
--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):
sampleAny of the optional columns above may be appended to the header when your data needs them: group, ref_fasta, ref_gff, use_ref, strategy, assembler, assembly_scaffolding_order, genome_size, flye_mode, flye_args, hifiasm_args, assembler_ont, assembler_ont_args, assembler_hifi, assembler_hifi_args, ontreads, ont_collect, ont_adapters, ont_fastplong_args, hifireads, hifi_adapters, hifi_fastplong_args, jellyfish, jellyfish_k, jellyfish_size, polish, polish_pilon, polish_dorado, polish_medaka, medaka_model, scaffold_longstitch, scaffold_links, scaffold_ragtag, scaffold_hic, hic_aligner, merqury, qc_reads, busco, busco_db, busco_lineage, quast, ref_map_bam, assembly, assembly_map_bam, csi_index_size, lift_annotations, use_short_reads, shortread_trim, meryl_k, shortread_F, shortread_R, paired, hic_trim, hic_F, hic_R.
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).
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 genomeassembler --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 = '!>=25.10.4'.
To pin this release's declared minimum engine — useful when a newer Nextflow has incompatible config parsing:
nfclaw run genomeassembler ... --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 genomeassembler --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.
sample| Column | Type | Required | Allowed / constraints |
|---|---|---|---|
sample | string | required | matches ^\S+$ |
group | string | optional | matches ^\S+$ |
ref_fasta | string (file path) | optional | — |
ref_gff | string (file path) | optional | — |
use_ref | boolean | optional | — |
strategy | string | optional | — |
assembler | string | optional | flyehifiasmflye_hifiasmhifiasm_hifiasmflye_flyehifiasm_flye |
assembly_scaffolding_order | string | optional | ont_on_hifihifi_on_ont |
genome_size | string | optional | — |
flye_mode | string | optional | --pacbio-raw--pacbio-corr--pacbio-hifi--nano-raw--nano-corr--nano-hq |
flye_args | string | optional | — |
hifiasm_args | string | optional | — |
assembler_ont | string | optional | — |
assembler_ont_args | string | optional | — |
assembler_hifi | string | optional | — |
assembler_hifi_args | string | optional | — |
ontreads | string (file path) | optional | — |
ont_collect | boolean | optional | — |
ont_adapters | string | optional | — |
ont_fastplong_args | string | optional | — |
hifireads | string (file path) | optional | — |
hifi_adapters | string | optional | — |
hifi_fastplong_args | string | optional | — |
jellyfish | boolean | optional | — |
jellyfish_k | integer | optional | — |
jellyfish_size | string | optional | — |
polish | string | optional | pilondoradomedakadorado+pilonmedaka+pilon |
polish_pilon | boolean | optional | — |
polish_dorado | boolean | optional | — |
polish_medaka | boolean | optional | — |
medaka_model | string | optional | — |
scaffold_longstitch | boolean | optional | — |
scaffold_links | boolean | optional | — |
scaffold_ragtag | boolean | optional | — |
scaffold_hic | boolean | optional | — |
hic_aligner | string | optional | bwa-mem2minimap2 |
merqury | boolean | optional | — |
qc_reads | string | optional | onthifi |
busco | boolean | optional | — |
busco_db | string (directory path) | optional | — |
busco_lineage | string | optional | — |
quast | boolean | optional | — |
ref_map_bam | string (file path) | optional | — |
assembly | string | optional | — |
assembly_map_bam | string (file path) | optional | — |
csi_index_size | integer | optional | — |
lift_annotations | boolean | optional | — |
use_short_reads | boolean | optional | — |
shortread_trim | boolean | optional | — |
meryl_k | integer | optional | ≥ 1 |
shortread_F | string (file path) | optional | — |
shortread_R | string (file path) | optional | — |
paired | boolean | optional | — |
hic_trim | boolean | optional | — |
hic_F | string (file path) | optional | — |
hic_R | string (file path) | optional | — |
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
72 parameters · 12 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.
58 parameters · 14 hidden
Annotations options1
Lift-over annotations (requires ref_gff).
Assembly options11
Assembler to use. Valid choices depend on strategy; for single either 'flye' or 'hifiasm', hybrid can be done with 'hifiasm' and for scaffolded assembly provide the names of the assemblers separated with an underscore. The first assembler will be used for ONT reads, the second for HiFi reads see below: asembler_ont and assembler_hifi.
assembler_hifi assembles HiFi reads. This option is mainly useful when building more complex samplesheets.
Arguments to be passed to assembler_hifi (HiFi).
assembler_ont assembles ONT reads. This option is mainly useful when building more complex samplesheets.
Arguments to be passed to assembler_ont (ONT)
When strategy is 'scaffold', which assembly should be scaffolded onto which?
Additional args for flye.
Flye assembly mode.
Expected genome size, optional.
Extra arguments passed to hifiasm
Assembly strategy to use. Valid choices are 'single', 'hybrid' and 'scaffold'.
Generic options2
Display the full detailed help message.
Display hidden parameters in the help message (only works when --help or --help_full are provided).
Hic options3
Path to forward HiC short reads.
Path to reverse HiC short reads.
Trim HiC short reads.
Input Output options3
Email address for completion summary.
Path to comma-separated file containing information about the samples in the experiment.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Long Read Preprocessing10
Adapters for HiFi read-trimming.
Additional args to be passed to fastplong for HiFi reads.
Path to HiFi reads.
Run jellyfish and genomescope (recommended).
Value of k used during k-mer analysis with jellyfish.
Initial hash size used by jellyfish count.
Adapters for ONT read-trimming.
Collect ONT reads from several files.
Additional args to be passed to fastplong for ONT reads.
Path to ONT reads.
Polishing options5
Model to use with medaka.
String describing the polishing strategy. Takes priority over boolean selectors. If missing will be created from boolean selectors.
Polish assembly with dorado (ONT only).
Polish assembly with medaka (ONT only).
Polish assembly with pilon. Requires short reads.
Qc options10
Can be used to provide existing assembly will skip assembly and perform downstream steps including QC.
A mapping (bam) of reads mapped to the provided assembly can be specified for QC. If provided, alignment to the provided assembly fasta will not run,
Run BUSCO.
Path to BUSCO data-base (optional).
BUSCO lineage to use.
Index size to use for csi index (default: 14), creating and index of size 2^csi_index_size. See samtools index documentation for details.
Run merqury if short reads are provided.
Long reads that should be used for QC when both ONT and HiFi reads are provided. Options are 'ont' or 'hifi'.
Run QUAST.
A mapping (bam) of reads mapped to the reference can be provided for QC. If provided, alignment to reference fasta will not run.
Reference Parameters2
Path to reference genome seqeunce (fasta)
Path to reference genome annotations (gff)
Scaffolding options5
Aligner to use for HiC reads; default: 'bwa-mem2'.
Scaffold using HiC reads using yahs (requires reads).
Scaffolding with links.
Scaffold with longstitch.
Scaffold with ragtag (requires reference).
Short Read options6
kmer length for meryl / merqury.
Are shortreads paired.
Path to forward short reads.
Path to reverse short reads.
Trim short reads.
Use short reads.
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/genomeassembler/blob/2.0.1/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.