Assembly: Snakemake

As mentioned on the Running Workflows page, the Snakemake workflows define build rules that trigger all of the rules composing a given workflow.

As a reminder, the Running Workflows page showed how to call Snakemake and ask for a particular target:

snakemake [FLAGS] <target>

You can replace <target> with any of the build rules below.

Build Rules

The build rules are the rules that the end user should be calling. A list of available build rules in the assembly workflow is given below.

assembly_workflow_metaspades

    Build rule: trigger the metaspades assembly step.

assembly_workflow_megahit

    Build rule: trigger the megahit assembly step.

assembly_workflow_all

    Build rule: trigger the assembly step with all assemblers.

Pass the name of the build rule directly to Snakemake on the command line:

snakemake [FLAGS] assembly_workflow_all

See below for how to configure these workflows. See the Quick Start for details on the process of running this workflow.

Snakemake Configuration Dictionary

There are three types of key-value pairs that can be set in the Snakemake configuration dictionary (also see the Workflow Configuration page).

Data Files Configuration

Set the files key to a dictionary containing a list of key-value pairs, where the keys are filenames and values are URLs:

{
    "files" : {
        "SRR606249_1_reads.fq.gz" :           "files.osf.io/v1/resources/dm938/providers/osfstorage/59f0f9156c613b026430dbc7",
        "SRR606249_2_reads.fq.gz" :           "files.osf.io/v1/resources/dm938/providers/osfstorage/59f0fc7fb83f69026076be47",
        "SRR606249_subset10_1_reads.fq.gz" :  "files.osf.io/v1/resources/dm938/providers/osfstorage/59f10134b83f69026377611b",
        "SRR606249_subset10_2_reads.fq.gz" :  "files.osf.io/v1/resources/dm938/providers/osfstorage/59f101f26c613b026330e53a",
        "SRR606249_subset25_1_reads.fq.gz" :  "files.osf.io/v1/resources/dm938/providers/osfstorage/59f1039a594d900263120c38",
        "SRR606249_subset25_2_reads.fq.gz" :  "files.osf.io/v1/resources/dm938/providers/osfstorage/59f104ed594d90026411f486",
        "SRR606249_subset50_1_reads.fq.gz" :  "files.osf.io/v1/resources/dm938/providers/osfstorage/59f1082d6c613b026430e5cf",
        "SRR606249_subset50_2_reads.fq.gz" :  "files.osf.io/v1/resources/dm938/providers/osfstorage/59f10ac6594d900262123e77",
    }
}

Put these in a JSON file (e.g., config/custom_datafiles.json in the workflows directory) and pass the name of the config file to Snakemake using the --configfile flag:

snakemake --configfile=config/custom_datafiles.json [FLAGS] <target>

Workflow Configuration

Set the workflows key of the Snakemake configuration dictionary to a dictionary containing details about the workflow you want to run. The workflow configuration values are values that will end up in the final output file's filename.

Here is the structure of the configuration dictionary for assembly workflows:

{
    "workflows" : {
        "assembly_workflow_metaspades" : {
            "sample"    : ["SRR606249_subset10","SRR606249_subset25"],
            "qual"      : ["2","30"],
        },

        "assembly_workflow_megahit" : {
            "sample"    : ["SRR606249_subset10","SRR606249_subset25"],
            "qual"      : ["2","30"],
        },

        "assembly_workflow_all" : {
            "sample"    : ["SRR606249_subset10","SRR606249_subset25"],
            "qual"      : ["2","30"],
        },

    }
}

The sample and qual keys are used by Snakemake to generate a list of input files required for the rule, and to generate the name of the output file from the workflow. These should be lists of strings. sample should match the read files listed in the files section, while qual should be the quality trimming value to use.

Put these in a JSON file (e.g., config/custom_workflowconfig.json in the workflows directory) and pass the name of the config file to Snakemake using the --configfile flag:

snakemake --configfile=config/custom_workflowconfig.json [FLAGS] <target>

Workflow Parameters

Set the assembly key of the Snakemake configuration dictionary as shown below:

{
    "assembly" : {
        "assembly_patterns" : {
            "metaspades_pattern" : "{sample}.trim{qual}_metaspades.contigs.fa",
            "megahit_pattern" : "{sample}.trim{qual}_megahit.contigs.fa",
            "assembly_pattern" : "{sample}.trim{qual}_{assembler}.contigs.fa",
            "quast_pattern" : "{sample}.trim{qual}_{assembler}_quast/report.html",
            "multiqc_pattern" : "{sample}.trim{qual}_{assembler}_multiqc/report.html",
        }
    }
}

To use custom values for these parameters, put the configuration dictionary above (or any subset of it) into a JSON file (e.g., config/custom_workflowparams.json in the workflows directory) and pass the name of the config file to Snakemake using the --configfile flag:

snakemake --configfile=config/custom_workflowparams.json [FLAGS] <target>