Command syntax¶
Every Aviary invocation has a command followed by that command's options:
aviary --verbosity 5 recover --assembly assembly.fasta \
-1 sample_R1.fastq.gz -2 sample_R2.fastq.gz --output results/
Global options must come before the command. Command options come after it.
Global options¶
These three options belong to the top-level aviary parser and are not valid
after a subcommand.
| Option | Value | Meaning |
|---|---|---|
--version |
none | Print the installed Aviary version and exit. |
--verbosity |
1–5 |
Set logging to critical, error, warning, info or debug. [default: 4] |
--log |
FILE |
Write logging to a new file. Aviary refuses to overwrite an existing file. |
aviary --version
aviary --verbosity 5 assemble -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz
aviary --log aviary.log complete -1 reads_R1.fastq.gz -2 reads_R2.fastq.gz
Help¶
For assemble, recover and complete, --help shows a concise command
summary and examples; use --full-help (or --full_help) for the complete
option list. The other commands show their complete option list with
--help.
Files and directories¶
Options shown as FILE [FILE ...] or DIR [DIR ...] accept a space-separated
list. Shell globs are also valid when they expand in the intended sample order:
aviary recover --assembly assembly.fasta \
-1 sample_A_R1.fastq.gz sample_B_R1.fastq.gz \
-2 sample_A_R2.fastq.gz sample_B_R2.fastq.gz
aviary cluster --input-runs runs/sample_A runs/sample_B runs/sample_C
Keep paired forward and reverse lists in matching order. Quote paths that
contain spaces. A value beginning with - must usually be quoted as part of a
single string, as with --snakemake-cmds and --pggb-params.
Boolean values¶
Boolean options accept either a bare flag or an explicit value:
aviary recover --assembly assembly.fasta -1 R1.fq.gz -2 R2.fq.gz --strict
aviary recover --assembly assembly.fasta -1 R1.fq.gz -2 R2.fq.gz --strict true
aviary recover --assembly assembly.fasta -1 R1.fq.gz -2 R2.fq.gz --clean false
A bare flag means true. Accepted true values are yes, true, t, y and
1; false values are no, false, f, n and 0, case-insensitively.
There are no --no-clean-style negated flags. This syntax applies to
--request-gpu, --strict, --dry-run, --clean, --build, --build-gpu,
--disable-adapter-trimming, --skip-qc, --use-unicycler, --use-megahit,
--coassemble, --binning-only, --skip-abundances, --skip-taxonomy,
--skip-singlem, --use-checkm2-scores and build --gpu.
Aliases¶
The reference uses the canonical hyphenated spelling. Aviary also accepts
underscore aliases for most multiword options, for example
--max-threads/--max_threads and --long-read-type/--long_read_type.
Prefer hyphens in scripts and publications because that is the spelling shown
in this manual and in normal help output.
Common non-mechanical aliases are:
| Canonical form | Also accepted |
|---|---|
--pe-1, --pe-2 |
-1, -2, --paired-reads-1, --paired-reads-2, --pe1, --pe2 |
--longreads |
-l, --long-reads, --long_reads |
--longread-type |
-z, --long-read-type, --long_read_type, --longread_type |
--tmpdir |
--tempdir, --tmp-dir, --tmp, --temp, --temp-dir and underscore forms |
--dry-run |
--dryrun, --dry_run |
--coassemble |
--co-assemble, --co_assemble |
--extra-binners |
singular --extra-binner and underscore forms |
--skip-binners |
singular --skip-binner and underscore forms |
Passing lists and option strings¶
List-valued options consume values until the next recognised Aviary option. Put them before the next flag, and do not comma-separate them:
aviary recover --assembly assembly.fasta \
--extra-binners concoct comebin \
--skip-binners vamb metabat
Options that forward a command fragment take one quoted string:
aviary recover --assembly assembly.fasta -1 R1.fq.gz -2 R2.fq.gz \
--snakemake-cmds "--printshellcmds --keep-going"
See Input files for all supported read layouts and Shared options for workflow, resource and output controls.