Read Filtering Workflow: 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 read filtering workflow is given below.

read_filtering_pretrim_workflow

    Build rule: trigger the read filtering workflow

read_filtering_posttrim_workflow

    Build rule: trigger the read filtering workflow

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

snakemake [FLAGS] read_filtering_pretrim_workflow read_filtering_posttrim_workflow

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 read filtering workflows (pre-trimming and post-trimming quality assessment):

{
    "workflows" : {

        "read_filtering_pretrim_workflow" : {
            "sample"    : ["SRR606249_subset10","SRR606249_subset25"]
        },

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

The sample list specifies the prefixes of the sample reads to run the read filtering workflow on. The qual list specifies the values to use for quality trimming (for the post-trimming workflow).

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 read_filtering key of the Snakemake configuration dictionary to a dictionary containing various child dictionaries and key-value pairs:

{
    "read_filtering" : {
        "read_patterns" : {
            "pre_trimming_pattern"  : "{sample}_{direction}_reads.fq.gz",
            "post_trimming_pattern" : "{sample}_{direction}.trim{qual}.fq.gz",
        },

        "direction_labels" : {
            "forward" : "1",
            "reverse" : "2"
        },

        "quality_assessment" : {
            "fastqc_suffix": "fastqc",
        },

        "quality_trimming" : {
            "trim_suffix" : "se"
        },

        "interleaving" : {
            "interleave_suffix" : "pe"
        },

        "adapter_file" : {
            "name" : "TruSeq2-PE.fa",
            "url"  : "http://dib-training.ucdavis.edu.s3.amazonaws.com/mRNAseq-semi-2015-03-04/TruSeq2-PE.fa"
        }
    }
}

The pre_trimming_pattern must match the filename pattern of the reads that are provided in the files key. The {sample} and {direction} notation is for Snakemake to match wildcards. For example, the pattern

    {sample}_{direction}_reads.fq.gz

will match the filename

    SRR606249_subset10_1_reads.fq.gz

such that the wildcard values are sample=SRR606249_subset10 and direction=1.

The direction_labels key is used to indicate the suffix used for forward and reverse reads; this is typically 1 and 2 but can be customized by the user if needed.

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>