richardstoeckl/prokanota

prokanota - Flexible pipeline for prokaryotic annotation

Overview

Latest release: 1.2.0, Last update: 2025-12-05

Linting: linting: failed, Formatting: formatting: failed

Deployment

Step 1: Install Snakemake and Snakedeploy

Snakemake and Snakedeploy are best installed via the Conda. 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/richardstoeckl/prokanota . --tag 1.2.0

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.

General configuration

To configure this workflow, modify config/config.yaml and config/metadata.csv according to your needs, following the explanations provided in the file.

Pipeline configuration

To successfully run the annotation pipeline, you will need to configure the paths to the databases and the output directories in the config/config.yaml file.

Sample setup

The sample setup is specified via comma-separated tabular file (.csv). Missing values can be specified by empty columns.

Sample sheet

The default sample sheet is config/metadata.csv (as configured in config/config.yaml). Each row usually corresponds to one genome with the first collumn being the sampleID (Note: The sampleID is used to name the output files and is used to calculate the gene_ids!), and the second column being the path to the genome assembly in FASTA format.

Linting and formatting

Linting results

  1No validator found for JSON Schema version identifier 'http://json-schema.org/draft-07/schema#'
  2Defaulting to validator for JSON Schema version 'https://json-schema.org/draft/2020-12/schema'
  3Note that schema file may not be validated correctly.
  4No validator found for JSON Schema version identifier 'http://json-schema.org/draft-07/schema#'
  5Defaulting to validator for JSON Schema version 'https://json-schema.org/draft/2020-12/schema'
  6Note that schema file may not be validated correctly.
  7Lints for snakefile /tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/parseSearchResults.smk:
  8    * Absolute path "/^#/d" in line 52:
  9      Do not define absolute paths inside of the workflow, since this renders
 10      your workflow irreproducible on other machines. Use path relative to the
 11      working directory instead, or make the path configurable via a config
 12      file.
 13      Also see:
 14      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
 15    * Absolute path "/^#/d" in line 111:
 16      Do not define absolute paths inside of the workflow, since this renders
 17      your workflow irreproducible on other machines. Use path relative to the
 18      working directory instead, or make the path configurable via a config
 19      file.
 20      Also see:
 21      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
 22    * Absolute path "/mnt/DATA/common/AnnotateGenomesDBs/arCOG/arCOGdef.tab" in line 140:
 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    * Absolute path "/^#/d" in line 172:
 30      Do not define absolute paths inside of the workflow, since this renders
 31      your workflow irreproducible on other machines. Use path relative to the
 32      working directory instead, or make the path configurable via a config
 33      file.
 34      Also see:
 35      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
 36    * Absolute path "/^#/d" in line 231:
 37      Do not define absolute paths inside of the workflow, since this renders
 38      your workflow irreproducible on other machines. Use path relative to the
 39      working directory instead, or make the path configurable via a config
 40      file.
 41      Also see:
 42      https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
 43
 44Lints for rule prepareCDDdb (line 30, /tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/prepDBs.smk):
 45    * No log directive defined:
 46      Without a log directive, all output will be printed to the terminal. In
 47      distributed environments, this means that errors are harder to discover.
 48      In local environments, output of concurrent jobs will be mixed and become
 49      unreadable.
 50      Also see:
 51      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 52    * Specify a conda environment or container for each rule.:
 53      This way, the used software for each specific step is documented, and the
 54      workflow can be executed on any machine without prerequisites.
 55      Also see:
 56      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 57      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 58
 59Lints for rule prepareCOGdb (line 70, /tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/prepDBs.smk):
 60    * No log directive defined:
 61      Without a log directive, all output will be printed to the terminal. In
 62      distributed environments, this means that errors are harder to discover.
 63      In local environments, output of concurrent jobs will be mixed and become
 64      unreadable.
 65      Also see:
 66      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 67    * Specify a conda environment or container for each rule.:
 68      This way, the used software for each specific step is documented, and the
 69      workflow can be executed on any machine without prerequisites.
 70      Also see:
 71      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
 72      https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
 73
 74Lints for rule preparePGAPdb (line 108, /tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/prepDBs.smk):
 75    * No log directive defined:
 76      Without a log directive, all output will be printed to the terminal. In
 77      distributed environments, this means that errors are harder to discover.
 78      In local environments, output of concurrent jobs will be mixed and become
 79      unreadable.
 80      Also see:
 81      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
 82
 83Lints for rule prepareARCOGdb (line 144, /tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/prepDBs.smk):
 84    * Param outdir 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 prepareARCOGdbMapping (line 175, /tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/prepDBs.smk):
 94    * No log directive defined:
 95      Without a log directive, all output will be printed to the terminal. In
 96      distributed environments, this means that errors are harder to discover.
 97      In local environments, output of concurrent jobs will be mixed and become
 98      unreadable.
 99      Also see:
100      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
101
102Lints for rule collectMasterTable (line 254, /tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/parseSearchResults.smk):
103    * No log directive defined:
104      Without a log directive, all output will be printed to the terminal. In
105      distributed environments, this means that errors are harder to discover.
106      In local environments, output of concurrent jobs will be mixed and become
107      unreadable.
108      Also see:
109      https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files

Formatting results

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 7	PEP8 recommends block comments appear before what they describe
 8(see https://www.python.org/dev/peps/pep-0008/#id30)
 9[DEBUG] In file "/tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/prepDBs.smk":  Formatted content is different from original
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11[DEBUG] In file "/tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/parseSearchResults.smk":  Formatted content is different from original
12[DEBUG] 
13[DEBUG] In file "/tmp/tmp8rywovgx/richardstoeckl-prokanota-c2dc892/workflow/rules/searchDBs.smk":  Formatted content is different from original
14[INFO] 5 file(s) would be changed 😬
15
16snakefmt version: 0.11.2