Microbial & metagenomicslatest-release

bacass

nf-core/bacass

Simple bacterial assembly and annotation

version2.7.0ce30c3a857Nov 3, 2026 Upstream Usage docs

Key tools

FastQCFastPPorechopFiltlongNanoPlotToulligQCpycoQCUnicyclerMEGAHITMiniasmRaconCanuFlyeRavenAutocyclerDragonflyeMinimap2QUASTProkkaBaktaDFASTLiftoffMedakaNanopolishBUSCOSAMtoolsKraken2KmerFinderRasusaMultiQC

Run it

nfclaw

nfclaw run bacass --input samplesheet.csv --outdir results -profile docker

raw nextflow

nextflow run pipelines/bacass/upstream -profile docker --input samplesheet.csv --outdir results

demo · bundled test profile

nfclaw run bacass --demo --outdir results   # adds the upstream test profile (-profile test,docker)

Inputs

column	type	required	constraints
`ID`	string	yes	matches `^\S+$`
`R1`	['string', 'null'] or string	no
`R2`	['string', 'null'] or string	no
`LongFastQ`	['string', 'null'] or string	no
`Fast5`	['string', 'null'] or string	no
`GenomeSize`	['string', 'null'] or string	no

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):

csv

ID

Any of the optional columns above may be appended to the header when your data needs them: R1, R2, LongFastQ, Fast5, GenomeSize.

From data files. --input may also be the data files — a directory (searched recursively), a quoted glob, or files (--input once per file) — from which nfclaw writes this samplesheet once you choose the read columns: the samplesheet takes reads in several column groups (R1 + R2; LongFastQ) and file names cannot tell which yours belong in; leave the groups you do not use empty, e.g. --sheet-set LongFastQ=. Set the required columns no file determines with --sheet-set COLUMN=VALUE. Preview it with --check; a run records it in <outdir>/provenance/ for replay.

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:

bash

nfclaw run bacass --input samplesheet.csv --outdir results -profile docker \
  --limit-cpus 4 --limit-memory 15.GB

nfclaw 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:

bash

nfclaw run bacass ... --nxf-ver 25.10.4

--nxf-ver is recorded in <outdir>/provenance/, so the replay uses the same engine. See known-issues.

Demo

bash

nfclaw run bacass --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.

samplesheet.csv header

ID

Column	Type	Required	Allowed / constraints
`ID`	string	required	matches ^\S+$
`R1`	['string', 'null'] or string	optional	—
`R2`	['string', 'null'] or string	optional	—
`LongFastQ`	['string', 'null'] or string	optional	—
`Fast5`	['string', 'null'] or string	optional	—
`GenomeSize`	['string', 'null'] or string	optional	—

Required parameters

--inputstring (file path)

Path to tab-separated sample sheet

--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 groups

Every 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.

Groups

nextflow_schema.json

59 parameters · 17 hidden

Annotation8

The annotation method to annotate the final assembly.

Path to Bakta database

Download Bakta database

This can be used to supply extra options to the Bakta download module

Specifies a configuration file for the DFAST annotation method.

Use the reference files (.fasta, .gff) from kmerfinder step for LIFTOFF.

Extra arguments for prokka annotation tool.

FASTA file with protein sequences to be used as reference by PROKKA.

Assembly Parameters13

The assembler(s) to use for assembly.

Assembly mode to use for all samples, or per-sample autodetection when set to auto.

Add the detected assembly type to output sample IDs in auto mode.

What assemblers to use for autocycler

Arguments to autocycler cluster.

Number of subsets to assemble.

Minimum depth for subsets to assemble.

This can be used to supply extra options to the Canu assembler. Will be ignored when other assemblers are used.

Allowed technologies for long read assembly with CANU.

Extra arguments for Dragonflye

Allowed technologies for long read assembly with Flye.

Extra arguments for MEGAHIT

Extra arguments for Unicycler

Assembly Polishing1

Which assembly polishing method to use.

Busco options5

Clean intermediate BUSCO files

Path to BUSCO config file

Path to BUSCO database

BUSCO lineage to use, you can use other BUSCO lineages, these are available in: busco.ezlab.org/list_of_lineages.html

BUSCO mode to use

Contamination Screening4

Path to the KmerFinder bacteria database (e.g. /path_to/kmerfinder/, /path_to/kmerfinder/bacteria/ or /path_to/kmerfinder/bacteria.tar.gz). Only taxonomic group bacteria is supported. If a directory is provided, the pipeline auto-detects whether it already includes the bacteria/ level. See installation guidelines: https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/. Example: --kmerfinderdb 'ftp://ftp.cbs.dtu.dk/public/CGE/databases/KmerFinder/version/latest/bacteria.tar.gz' (FTP download is ~30GB and can be slow; prefer pre-downloading and passing a local .tar.gz). Older version: https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz.

Path to Kraken2 database.

Reference FASTA file.

Reference GFF file.

Generic options5

Display the help message.

Display the full detailed help message.

Custom MultiQC yaml file containing HTML including a methods description.

MultiQC report title. Printed as page header, used for filename if not otherwise specified.

Display hidden parameters in the help message (only works when --help or --help_full are provided).

Input Output options3

Email address for completion summary.

Path to tab-separated sample sheet

The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.

Qc And Trim13

Specify true to not write any reads that pass trimming thresholds.This can be used to use fastp for the output report only.

This can be used to pass arguments to Fastp

Arguments for running Filtlong

Minimun length for Filtlong to work

Tool for ONT read filtering

Use Rasusa to downsample reads to a target coverage

Target coverage for Rasusa read downsampling

save trimmed files

save files that failed to pass trimming thresholds ending in *.fail.fastq.gz

Skip FastP

Skip FastQC

Skip Nanoplot

Skip ToulligQC

Skipping options7

Skip annotating the assembly with Prokka /DFAST.

Skip BUSCO

Skip contamination analysis with Kmerfinder

Skip running Kraken2 classifier on reads.

Skip MultiQC

Skip Medaka or Nanopolish polishing for long-read and hybrid assemblies.

Skip running PycoQC on long read input.

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. --skip-multiqc true disables that report. 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/bacass/blob/2.7.0/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.