usnistgov/defrabb

Genome In A Bottle Development Framework for Assembly Based Benchmarks

Overview

Latest release: None, Last update: 2026-07-30

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

Quality control: linting: failed formatting: failed

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 options

defrabb uses two configuration files

See schema/analyses-schema.yml and schema/resources-schema.yml for detailed descriptions and field formats requirements.

resource.yaml

used to define:

  • parameters, threads, and memory for compute intensive steps

  • urls for remote files: diploid assemblies, genome reference files, stratifications, and callsets used to evaluate draft benchmark

  • exclusion sets and how they are applied

Analyses Tables

Provides run specific configurations

  • input diploid assembly

  • version of reference genome

  • assembly-based variant caller and parameters

  • vcf and bed processing including what exclusions to use

  • benchmarking method and comparison callset used for initial evaluation

Linting and formatting

Linting results
  1/tmp/tmpa3xn176p/rules/bench_vcf_normalize.smk:77: SyntaxWarning: invalid escape sequence '\|'
  2  """
  3/tmp/tmpa3xn176p/rules/bench_vcf_normalize.smk:90: SyntaxWarning: invalid escape sequence '\|'
  4  ref=get_ref_file,
  5Lints for snakefile /tmp/tmpa3xn176p/rules/helpers_bench.smk:
  6    * Mixed rules and functions in same snakefile.:
  7      Small one-liner functions used only once should be defined as lambda
  8      expressions. Other functions should be collected in a common module, e.g.
  9      'rules/common.smk'. This makes the workflow steps more readable.
 10      Also see:
 11      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
 12
 13Lints for snakefile /tmp/tmpa3xn176p/rules/exclusions_self_discrep.smk:
 14    * Mixed rules and functions in same snakefile.:
 15      Small one-liner functions used only once should be defined as lambda
 16      expressions. Other functions should be collected in a common module, e.g.
 17      'rules/common.smk'. This makes the workflow steps more readable.
 18      Also see:
 19      https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html#includes
 20
 21Lints for snakefile /tmp/tmpa3xn176p/rules/stratifications_genome_specific.smk:
 22    * Absolute path "/{ref_id}_{asm_id}_{bench_type}_{vc_cmd}-{vc_param_id}." in line 33:
 23      Do not define absolute paths inside of the workflow, since this renders
 24      your workflow irreproducible on other machines. Use path relative to the
 25      working directory instead, or make the path configurable via a config
 26      file.
 27      Also see:
 28      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
 29    * Path composition with '+' in line 33:
 30      This becomes quickly unreadable. Usually, it is better to endure some
 31      redundancy against having a more readable workflow. Hence, just repeat
 32      common prefixes. If path composition is unavoidable, use pathlib or
 33      (python >= 3.6) string formatting with f"...".
 34    * Path composition with '+' in line 45:
 35      This becomes quickly unreadable. Usually, it is better to endure some
 36      redundancy against having a more readable workflow. Hence, just repeat
 37      common prefixes. If path composition is unavoidable, use pathlib or
 38      (python >= 3.6) string formatting with f"...".
 39    * Path composition with '+' in line 64:
 40      This becomes quickly unreadable. Usually, it is better to endure some
 41      redundancy against having a more readable workflow. Hence, just repeat
 42      common prefixes. If path composition is unavoidable, use pathlib or
 43      (python >= 3.6) string formatting with f"...".
 44    * Path composition with '+' in line 106:
 45      This becomes quickly unreadable. Usually, it is better to endure some
 46      redundancy against having a more readable workflow. Hence, just repeat
 47      common prefixes. If path composition is unavoidable, use pathlib or
 48      (python >= 3.6) string formatting with f"...".
 49
 50Lints for rule pav_config (line 105, /tmp/tmpa3xn176p/rules/asm-varcall.smk):
 51    * Specify a conda environment or container for each rule.:
 52      This way, the used software for each specific step is documented, and the
 53      workflow can be executed on any machine without prerequisites.
 54      Also see:
 55      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 56      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 57
 58Lints for rule run_pav (line 134, /tmp/tmpa3xn176p/rules/asm-varcall.smk):
 59    * Param outdir is a prefix of input or output file but hardcoded:
 60      If this is meant to represent a file path prefix, it will fail when
 61      running workflow in environments without a shared filesystem. Instead,
 62      provide a function that infers the appropriate prefix from the input or
 63      output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
 64      Also see:
 65      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 66      https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
 67
 68Lints for rule standardize_vcasm_output (line 209, /tmp/tmpa3xn176p/rules/asm-varcall.smk):
 69    * No log directive defined:
 70      Without a log directive, all output will be printed to the terminal. In
 71      distributed environments, this means that errors are harder to discover.
 72      In local environments, output of concurrent jobs will be mixed and become
 73      unreadable.
 74      Also see:
 75      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 76    * Specify a conda environment or container for each rule.:
 77      This way, the used software for each specific step is documented, and the
 78      workflow can be executed on any machine without prerequisites.
 79      Also see:
 80      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 81      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 82
 83Lints for rule self_discrep_happy (line 42, /tmp/tmpa3xn176p/rules/exclusions_self_discrep.smk):
 84    * Param prefix is a prefix of input or output file but hardcoded:
 85      If this is meant to represent a file path prefix, it will fail when
 86      running workflow in environments without a shared filesystem. Instead,
 87      provide a function that infers the appropriate prefix from the input or
 88      output file, e.g.: lambda w, input: os.path.splitext(input[0])[0]
 89      Also see:
 90      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#non-file-parameters-for-rules
 91      https://snakemake.readthedocs.io/en/stable/tutorial/advanced.html#tutorial-input-functions
 92
 93Lints for rule write_report_params (line 96, /tmp/tmpa3xn176p/rules/report.smk):
 94    * Specify a conda environment or container for each rule.:
 95      This way, the used software for each specific step is documented, and the
 96      workflow can be executed on any machine without prerequisites.
 97      Also see:
 98      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 99      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
100
101Lints for rule install_dfam_hmm (line 177, /tmp/tmpa3xn176p/rules/bench_vcf_anno.smk):
102    * No log directive defined:
103      Without a log directive, all output will be printed to the terminal. In
104      distributed environments, this means that errors are harder to discover.
105      In local environments, output of concurrent jobs will be mixed and become
106      unreadable.
107      Also see:
108      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
Formatting results
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11[DEBUG] In file "/tmp/tmpa3xn176p/rules/asm-varcall.smk":  Formatted content is different from original
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19<unknown>:4: SyntaxWarning: invalid escape sequence '\|'
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22[INFO] 2 file(s) would be changed 😬
23[INFO] 16 file(s) would be left unchanged 🎉
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25snakefmt version: 0.11.5