https://github.com/bialimed/snake-basket

Customisable rules for snakemake.
https://github.com/bialimed/snake-basket

snakemake

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Customisable rules for snakemake.

• Host: GitHub
• URL: https://github.com/bialimed/snake-basket
• Owner: bialimed
• License: gpl-3.0
• Created: 2021-06-04T09:23:50.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2025-05-30T11:52:53.000Z (about 1 year ago)
• Last Synced: 2025-05-30T16:05:47.254Z (about 1 year ago)
• Topics: snakemake
• Language: Python
• Homepage:
• Size: 212 KB
• Stars: 2
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.txt

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README

          
# snake-basket

![license](https://img.shields.io/badge/license-GPLv3-blue)

## Description

This project provides multiples customizable rules for the workflow manager

[Snakemake](https://snakemake.readthedocs.io/en/stable/#). These rules have

built as python function and can be imported (with snakemake include) and

parametrized (with argument of the function).

## Usage

In this paragraph we will add a rule **markDuplicates** in your workflow.

### 1. Import the rule

  * Copy the rule in your workflow `rules` folder

         workflow_folder/

            rules/

                markDuplicates.smk          

            Snakemake

  * Add the rule in the list of imports `rules/all.smk`

    Add all.smk in rules (once by workflow)

         workflow_folder/

            rules/

                all.smk

                markDuplicates.smk

            Snakemake

    Add the rule in all.smk (it contains all the rules to import)

         ...

         include: "markDuplicates.smk"

         ...

  * Import all the wrapper functions in your `Snakefile`

         ...

         include: "rules/all.smk"

         ...

  The function `markDuplicates()` is now accessibe in your workflow.

### 2. Call rule in your workflow

  Add the function call and parameters in your code:

        ...

        markDuplicates(

            params_stringency="STRICT"

            params_keep_outputs=True

        )

        ...

  All accessible parameters and their default values are presented in function

  declaration of the rule in `markDuplicates.smk`. The main categories of these

  parameters are:

    * *input_*,

    * *output_*,

    * *param_*,

    * *snake_*: for parameters related to the Snakemake element like wildcards

    restrictions.

  Keep in mind that input and ouput must be consistent in terms of wildcards

  like with a standard rule.

### 3. Set execution environment for the rule

You can provide software of the rule by one of this three ways:

  * The software folder is in `$PATH`.

  * The path of the software is in workflow configuration file:

          ...

          software_paths:

              picard: /home/user/bin/picard

          ...

    *The name of the parameter is in bin_path argument of the `params` section

    of the rule in the `markDuplicates.smk`.*

  * You use conda environment with Snakemake (see option `--use-conda`) and

  the environment of your rule is in `envs` folder:

          workflow_folder/

              envs/

                  picard.yml

              rules/

                  all.smk

                  markDuplicates.smk

              Snakemake

     *The name of the environment file can be found in `conda` section of the

     rule in the `markDuplicates.smk`.*

### 4. *Configure the computing requirements [optional]*

Optional in local and required with cluster submission.

  

Default value are stored in rule in `resources` section:

    resources:

        extra = "",            # options added to cluster submission (example: "--qos=project_A")

        mem = "8G",            # maximum memory required

        partition = "normal"   # partition/queue name for job

    threads: 1                 # threads per job

Declare parameter usage in snakemake command line:

    snakemake \

      ...

      --cluster 'sbatch {resources.extra} --mem={resources.mem} --partition={resources.partition} --cpus-per-task={threads}'

##### Change default value by command line [recommended]

Values can be changed by `--set-threads` and `--set-resources` in snakemake

command line.

    snakemake \

      ...

      --cluster 'sbatch {resources.extra} --mem={resources.mem} --partition={resources.partition} --cpus-per-task={threads}' \

      --set-threads $RULE=$NUM \

      --set-resources $RULE:$KEY=$VAL $RULE:$KEY=$VAL \

##### Change default value by profile

You can change default values in profile configuration file.

    $PROFILE/config.yaml

        cluster: sbatch

        cluster: "sbatch {resources.extra} --mem={resources.mem} --partition={resources.partition} --cpus-per-task={threads}"

        set-resources:

            - $RULE:$KEY=$VAL

## Copyright

2019 Laboratoire d'Anatomo-Cytopathologie du CHU Toulouse