richardstoeckl/prokanota
prokanota - Flexible pipeline for prokaryotic annotation
Overview
Topics:
Latest release: 1.1.0, Last update: 2025-07-01
Linting: linting: failed, Formatting: formatting: failed
Deployment
Step 1: Install Snakemake and Snakedeploy
Snakemake and Snakedeploy are best installed via the Mamba package manager (a drop-in replacement for conda). If you have neither Conda nor Mamba, it is recommended to install Miniforge. More details regarding Mamba can be found here.
When using Mamba, run
mamba create -c conda-forge -c bioconda --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
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 1.1.0
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
1Lints for snakefile /tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/parseSearchResults.smk:
2 * Absolute path "/^#/d" in line 52:
3 Do not define absolute paths inside of the workflow, since this renders
4 your workflow irreproducible on other machines. Use path relative to the
5 working directory instead, or make the path configurable via a config
6 file.
7 Also see:
8 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
9 * Absolute path "/^#/d" in line 111:
10 Do not define absolute paths inside of the workflow, since this renders
11 your workflow irreproducible on other machines. Use path relative to the
12 working directory instead, or make the path configurable via a config
13 file.
14 Also see:
15 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
16 * Absolute path "/mnt/DATA/common/AnnotateGenomesDBs/arCOG/arCOGdef.tab" in line 140:
17 Do not define absolute paths inside of the workflow, since this renders
18 your workflow irreproducible on other machines. Use path relative to the
19 working directory instead, or make the path configurable via a config
20 file.
21 Also see:
22 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
23 * Absolute path "/^#/d" in line 172:
24 Do not define absolute paths inside of the workflow, since this renders
25 your workflow irreproducible on other machines. Use path relative to the
26 working directory instead, or make the path configurable via a config
27 file.
28 Also see:
29 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
30 * Absolute path "/^#/d" in line 231:
31 Do not define absolute paths inside of the workflow, since this renders
32 your workflow irreproducible on other machines. Use path relative to the
33 working directory instead, or make the path configurable via a config
34 file.
35 Also see:
36 https://snakemake.readthedocs.io/en/latest/snakefiles/configuration.html#configuration
37
38Lints for rule prepareCDDdb (line 30, /tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/prepDBs.smk):
39 * No log directive defined:
40 Without a log directive, all output will be printed to the terminal. In
41 distributed environments, this means that errors are harder to discover.
42 In local environments, output of concurrent jobs will be mixed and become
43 unreadable.
44 Also see:
45 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
46 * Specify a conda environment or container for each rule.:
47 This way, the used software for each specific step is documented, and the
48 workflow can be executed on any machine without prerequisites.
49 Also see:
50 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
51 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
52
53Lints for rule prepareCOGdb (line 70, /tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/prepDBs.smk):
54 * No log directive defined:
55 Without a log directive, all output will be printed to the terminal. In
56 distributed environments, this means that errors are harder to discover.
57 In local environments, output of concurrent jobs will be mixed and become
58 unreadable.
59 Also see:
60 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
61 * Specify a conda environment or container for each rule.:
62 This way, the used software for each specific step is documented, and the
63 workflow can be executed on any machine without prerequisites.
64 Also see:
65 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#integrated-package-management
66 https://snakemake.readthedocs.io/en/latest/snakefiles/deployment.html#running-jobs-in-containers
67
68Lints for rule preparePGAPdb (line 108, /tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/prepDBs.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
77Lints for rule prepareARCOGdb (line 144, /tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/prepDBs.smk):
78 * Param outdir 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 prepareARCOGdbMapping (line 175, /tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/prepDBs.smk):
88 * No log directive defined:
89 Without a log directive, all output will be printed to the terminal. In
90 distributed environments, this means that errors are harder to discover.
91 In local environments, output of concurrent jobs will be mixed and become
92 unreadable.
93 Also see:
94 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
95
96Lints for rule collectMasterTable (line 254, /tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/parseSearchResults.smk):
97 * No log directive defined:
98 Without a log directive, all output will be printed to the terminal. In
99 distributed environments, this means that errors are harder to discover.
100 In local environments, output of concurrent jobs will be mixed and become
101 unreadable.
102 Also see:
103 https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files
Formatting results
1[DEBUG]
2[DEBUG] In file "/tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/searchDBs.smk": Formatted content is different from original
3[DEBUG]
4[DEBUG] In file "/tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/parseSearchResults.smk": Formatted content is different from original
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6[DEBUG] In file "/tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/prepProteins.smk": Formatted content is different from original
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8[DEBUG] In file "/tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/Snakefile": Formatted content is different from original
9[DEBUG]
10[WARNING] In file "/tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/prepDBs.smk": Keyword "output" at line 156 has comments under a value.
11 PEP8 recommends block comments appear before what they describe
12(see https://www.python.org/dev/peps/pep-0008/#id30)
13[DEBUG] In file "/tmp/tmp47pq5vhm/richardstoeckl-prokanota-a6b001a/workflow/rules/prepDBs.smk": Formatted content is different from original
14[INFO] 5 file(s) would be changed 😬
15
16snakefmt version: 0.11.0