Comparison: 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>

Build Rules

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

List of available build rules in the comparison workflow:

comparison_workflow_reads

    Build rule: run sourmash compare on all reads

comparison_workflow_assembly

    Build rule: run sourmash compare on all assemblies

comparison_workflow_reads_assembly

    Build rule: run sourmash compare on all reads and assemblies together

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

snakemake [FLAGS] comparison_workflow_reads \
        comparison_workflow_assembly \
        comparison_workflow_reads_assembly

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 taxonomic classification workflows:

{
    "workflows" : {
        "comparison_workflow_reads": {
            #
            # these parameters determine which reads
            # the comparison workflow will be run on
            # 
            "kvalue"    : ["21","31","51"],
        },

        "comparison_workflow_assembly" : {
            #
            # these parameters determine which assembled reads
            # the comparison workflow will be run on
            # 
            "kvalue"    : ["21","31","51"],
        },

        "comparison_workflow_reads_assembly" : {
            #
            # these parameters determine which reads and assembled 
            # reads the comparison workflow will be run on
            # 
            "kvalue"    : ["21","31","51"],
        }
    }
}

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 taxonomic_classification key of the Snakemake configuration dictionary as shown below:

{
    "comparison" : {
        "compute_read_signatures" : {
            "scale"         : 10000,
            "kvalues"       : [21,31,51],
            "qual"          : ["2","30"],
            "sig_suffix"    : "_scaled10k.k21_31_51.sig", 
            "merge_suffix"  : "_scaled10k.k21_31_51.fq.gz"
        },
        "compare_read_signatures" : {
            "samples" : ["SRR606249_subset10","SRR606249_subset25"],
            "csv_out" : "SRR606249allsamples_trim2and30_read_comparison.k{kvalue}.csv"
        },
        "compute_assembly_signatures" : {
            "scale"         : 10000,
            "kvalues"       : [21,31,51],
            "qual"          : ["2","30"],
            "sig_suffix" : "_scaled10k.k21_31_51.sig",
            "merge_suffix"  : "_scaled10k.k21_31_51.fq.gz"
        },
        "compare_assembly_signatures" : {
            "samples"   : ["SRR606249_subset10","SRR606249_subset25"],
            "assembler" : ["megahit","metaspades"],
            "csv_out"   : "SRR606249_trim2and30_assembly_comparison.k{kvalue}.csv"
        },
        "compare_read_assembly_signatures" : {
            "samples"   : ["SRR606249_subset10"],
            "assembler" : ["megahit","metaspades"],
            "kvalues"   : [21, 31, 51],
            "csv_out"   : "SRR606249_trim2and30_ra_comparison.k{kvalue}.csv"
        }
    }
}

(Note that there are multiple "k values" being specified here, but these correspond to different steps in the workflow. The kvalues key in the compute_read_signatures and compute_assembly_signatures section provides the k values used in the intermediate steps of the workflow, and should be a superset of the the k values provided to the build rule.

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>