usnistgov/defrabb

Genome In A Bottle Development Framework for Assembly Based Benchmarks

Overview

Latest release: None, Last update: 2026-10-06

Share link: https://snakemake.github.io/snakemake-workflow-catalog?wf=usnistgov/defrabb

Quality control: linting: failed formatting: passed

Wrappers: bio/assembly-stats bio/bcftools/index bio/bcftools/sort bio/bedtools/intersect bio/bedtools/sort bio/bwa/index bio/samtools/faidx bio/samtools/index

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda package manager. It is recommended to install conda via Miniforge. Run

conda create -c conda-forge -c bioconda -c nodefaults --name snakemake snakemake snakedeploy

to install both Snakemake and Snakedeploy in an isolated environment. For all following commands ensure that this environment is activated via

conda activate snakemake

For other installation methods, refer to the Snakemake and Snakedeploy documentation.

Step 2: Deploy workflow

With Snakemake and Snakedeploy installed, the workflow can be deployed as follows. First, create an appropriate project working directory on your system and enter it:

mkdir -p path/to/project-workdir
cd path/to/project-workdir

In all following steps, we will assume that you are inside of that directory. Then run

snakedeploy deploy-workflow https://github.com/usnistgov/defrabb . --tag None

Snakedeploy will create two folders, workflow and config. The former contains the deployment of the chosen workflow as a Snakemake module, the latter contains configuration files which will be modified in the next step in order to configure the workflow to your needs.

Step 3: Configure workflow

To configure the workflow, adapt config/config.yml to your needs following the instructions below.

Step 4: Run workflow

The deployment method is controlled using the --software-deployment-method (short --sdm) argument.

To run the workflow with automatic deployment of all required software via conda/mamba, use

snakemake --cores all --sdm conda

Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment in step 2.

For further options such as cluster and cloud execution, see the docs.

Step 5: Generate report

After finalizing your data analysis, you can automatically generate an interactive visual HTML report for inspection of results together with parameters and code inside of the browser using

snakemake --report report.zip

Configuration

The following section is imported from the workflow’s config/README.md.

Configuration files

  • resources.yml: input URLs, named parameter profiles, exclusion definitions, and compute resources

  • analyses.tsv: default chr21 test analyses table

  • analyses_YYYYMMDD_v#.###_<id>.tsv: analyses tables for past production runs (do not edit)

  • sweeps/: parameter sweep configs for scripts/generate_param_sweep.py

  • release.json: template S3 release settings for run_defrabb release (NIST defaults are in profiles/nist/)

See docs/configuration.md for field definitions and compute resource settings. The schemas are in schema/.

Linting and formatting

Linting results
  1/home/runner/work/snakemake-workflow-catalog/snakemake-workflow-catalog/.pixi/envs/default/lib/python3.13/site-packages/google/auth/transport/grpc.py:43: FutureWarning: grpcio < 1.83.0 does not support Post-Quantum Cryptography (PQC). Support for non-PQC environments is deprecated. In April 2027, google-auth will raise its minimum requirements to enforce grpcio >= 1.83.0. For more details on Google Cloud's post-quantum security migration, visit: https://cloud.google.com/security/resources/post-quantum-cryptography
  2  warnings.warn(
  3/tmp/tmp3bidmw5f/rules/bench_vcf_normalize.smk:78: SyntaxWarning: invalid escape sequence '\|'
  4  """
  5/tmp/tmp3bidmw5f/rules/bench_vcf_normalize.smk:91: SyntaxWarning: invalid escape sequence '\|'
  6  ref=get_ref_file,
  7Lints for snakefile /tmp/tmp3bidmw5f/rules/helpers_varcall.smk:
  8    * Path composition with '+' in line 4:
  9      This becomes quickly unreadable. Usually, it is better to endure some
 10      redundancy against having a more readable workflow. Hence, just repeat
 11      common prefixes. If path composition is unavoidable, use pathlib or
 12      (python >= 3.6) string formatting with f"...".
 13
 14Lints for snakefile /tmp/tmp3bidmw5f/rules/helpers_bench.smk:
 15    * Mixed rules and functions in same snakefile.:
 16      Small one-liner functions used only once should be defined as lambda
 17      expressions. Other functions should be collected in a common module, e.g.
 18      'rules/common.smk'. This makes the workflow steps more readable.
 19      Also see:
 20      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
 21
 22Lints for snakefile /tmp/tmp3bidmw5f/rules/exclusions_self_discrep.smk:
 23    * Mixed rules and functions in same snakefile.:
 24      Small one-liner functions used only once should be defined as lambda
 25      expressions. Other functions should be collected in a common module, e.g.
 26      'rules/common.smk'. This makes the workflow steps more readable.
 27      Also see:
 28      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
 29
 30Lints for snakefile /tmp/tmp3bidmw5f/rules/stratifications_genome_specific.smk:
 31    * Absolute path "/{ref_id}_{asm_id}_{bench_type}_{vc_cmd}-{vc_param_id}." in line 34:
 32      Do not define absolute paths inside of the workflow, since this renders
 33      your workflow irreproducible on other machines. Use path relative to the
 34      working directory instead, or make the path configurable via a config
 35      file.
 36      Also see:
 37      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
 38    * Path composition with '+' in line 34:
 39      This becomes quickly unreadable. Usually, it is better to endure some
 40      redundancy against having a more readable workflow. Hence, just repeat
 41      common prefixes. If path composition is unavoidable, use pathlib or
 42      (python >= 3.6) string formatting with f"...".
 43    * Path composition with '+' in line 46:
 44      This becomes quickly unreadable. Usually, it is better to endure some
 45      redundancy against having a more readable workflow. Hence, just repeat
 46      common prefixes. If path composition is unavoidable, use pathlib or
 47      (python >= 3.6) string formatting with f"...".
 48    * Path composition with '+' in line 74:
 49      This becomes quickly unreadable. Usually, it is better to endure some
 50      redundancy against having a more readable workflow. Hence, just repeat
 51      common prefixes. If path composition is unavoidable, use pathlib or
 52      (python >= 3.6) string formatting with f"...".
 53    * Path composition with '+' in line 116:
 54      This becomes quickly unreadable. Usually, it is better to endure some
 55      redundancy against having a more readable workflow. Hence, just repeat
 56      common prefixes. If path composition is unavoidable, use pathlib or
 57      (python >= 3.6) string formatting with f"...".
 58
 59Lints for rule pav_config (line 104, /tmp/tmp3bidmw5f/rules/asm-varcall.smk):
 60    * Specify a conda environment or container for each rule.:
 61      This way, the used software for each specific step is documented, and the
 62      workflow can be executed on any machine without prerequisites.
 63      Also see:
 64      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 65      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 66
 67Lints for rule run_pav (line 137, /tmp/tmp3bidmw5f/rules/asm-varcall.smk):
 68    * Param outdir is a prefix of input or output file but hardcoded:
 69      If this is meant to represent a file path prefix, it will fail when
 70      running workflow in environments without a shared filesystem. Instead,
 71      provide a function that infers the appropriate prefix from the input or
 72      output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
 73      Also see:
 74      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 75      https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
 76
 77Lints for rule self_discrep_happy (line 42, /tmp/tmp3bidmw5f/rules/exclusions_self_discrep.smk):
 78    * Param prefix is a prefix of input or output file but hardcoded:
 79      If this is meant to represent a file path prefix, it will fail when
 80      running workflow in environments without a shared filesystem. Instead,
 81      provide a function that infers the appropriate prefix from the input or
 82      output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
 83      Also see:
 84      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 85      https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
 86
 87Lints for rule write_report_params (line 96, /tmp/tmp3bidmw5f/rules/report.smk):
 88    * Specify a conda environment or container for each rule.:
 89      This way, the used software for each specific step is documented, and the
 90      workflow can be executed on any machine without prerequisites.
 91      Also see:
 92      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 93      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 94
 95Lints for rule install_dfam_hmm (line 177, /tmp/tmp3bidmw5f/rules/bench_vcf_anno.smk):
 96    * No log directive defined:
 97      Without a log directive, all output will be printed to the terminal. In
 98      distributed environments, this means that errors are harder to discover.
 99      In local environments, output of concurrent jobs will be mixed and become
100      unreadable.
101      Also see:
102      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
Formatting results
All tests passed!