pangenome
nf-core/pangenome
The pangenome graph construction pipeline renders a collection of sequences into a pangenome graph. Its goal is to build a graph that is locally directed and acyclic while preserving large-scale variation. Maintaining local linearity is important for interpretation, visualization, mapping, comparative genomics, and reuse of pangenome graphs
Key tools
Run it
nfclaw run pangenome --input <input> --outdir results --n-haplotypes <n_haplotypes> -profile dockernextflow run pipelines/pangenome/upstream -profile docker --input <input> --outdir results --n_haplotypes <n_haplotypes>nfclaw run pangenome --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 BGZIPPED input FASTA to build the pangenome graph from. 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 pangenome --input <input> --outdir results --n-haplotypes <n_haplotypes> -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 pangenome ... --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 pangenome --demo --outdir results # adds the upstream test profile (-profile test,docker)Required parameters
--inputstring (file path)Path to BGZIPPED input FASTA to build the pangenome graph from.
Constraint · matches ^\S+\.fn?a(sta)?(\.gz)?$
--n-haplotypesnumberThe number of haplotypes in the input FASTA.
--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
63 parameters · 8 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.
33 parameters · 30 hidden
Community1
Enable community detection.
Generic options1
Custom MultiQC yaml file containing HTML including a methods description.
Input Output options5
Email address for completion summary.
Path to BGZIPPED input FASTA to build the pangenome graph from.
MultiQC report title. Printed as page header, used for filename if not otherwise specified.
The number of haplotypes in the input FASTA.
The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.
Seqwish options4
Ignores exact matches below this length.
Input PAF file. The wfmash alignment step is skipped.
Keep this randomly selected fraction of input matches.
Number of base pairs to use for transitive closure batch.
Smoothxg options9
Skip the graph smoothing step of the pipeline.
Path depth at which we don't pad the POA problem.
Number of CPUs for the potentially very memory expensive POA phase of SMOOTHXG. Default is 'task.cpus'.
Maximum sequence length to put int POA. Is a comma-separated list. For each integer, SMOOTHXG wil be executed once.
Pad each end of each seuqence in POA with 'smoothxg_poa_padding * longest_poa_seq' base pairs.
Score parameters for POA in the form of 'match,mismatch,gap1,ext1,gap2,ext2'. It may also be given as presets: 'asm5', 'asm10', 'asm15', 'asm20'. [default: 1,19,39,3,81,1 = asm5].
Run abPOA. [default: SPOA].
Run the POA in global mode. [default: local mode].
Write MAF output representing merged POA blocks.
Vg Deconstruct options1
Specify a set of VCFs to produce with --vcf_spec "REF[:LEN][,REF[:LEN]]*".
Wfmash options12
Minimum block length filter for mapping.
The number of files to generate from the approximate wfmash mappings to scale across a whole cluster. It is recommended to set this to the number of available nodes. If only one machine is available, leave it at 1.
Skip mappings between sequences with the same name prefix before the given delimiter character. This can be helpful if several sequences originate from the same chromosome. It is recommended that the sequence names respect the github.com/pangenome/PanSN-spec. In future versions of the pipeline it will be required that the sequence names follow this specification.
Filter out mappings unlikely to be this Average Nucleotide Identity (ANI) less than the best mapping.
Percent identity in the wfmash mashmap step.
Kmer size for mashmap.
Ignore the top % most-frequent kmers.
Merge successive mappings.
Number of mappings for each segment. [default: n_haplotypes - 1].
If this parameter is set, only the wfmash alignment step of the pipeline is executed. This option is offered for users who want to run wfmash on a cluster.
Segment length for mapping.
Keep this fraction of mappings (auto for giant component heuristic).
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/pangenome/blob/1.1.3/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.