FastQC is a quality control tool for genomic sequence data. See their website for more details.

Function Call

toolchest.fastqc(
    inputs,
    output_path=None,
    contaminants=None,
    adapters=None,
    limits=None,
    tool_args="",
    is_async=False,
)
toolchest$fastqc(
    inputs,
    output_path = NULL,
    tool_args = "",
    contaminants=NULL,
    adapters=NULL,
    limits=NULL,
    is_async = FALSE
)

Function Arguments

Argument

Use in place of:

Description

inputs

input file location

Path to one or more files to use as input.
SAM, BAM, or FASTQ formats are supported, as well as gzip-compressed variants. The files can be a local or remote, see Inputs and Outputs.

output_path

-o directory name

(optional) Path (directory) to where the output files will be downloaded. If omitted, skips download. The files can be a local or remote, see Inputs and Outputs.

contaminants

-c or --contaminants file path

(optional) Path to a custom contaminants file.

adapters

-a or --adapters file path

(optional) Path to a custom adapters file.

limits

-l or --limits file path

(optional) Path to a custom limits file.

tool_args

all other arguments

(optional) Additional arguments to be passed to FastQC. This should be a string of arguments like the command line.

is_async

Whether to run a job asynchronously. See Async Runs for more.

Output Files

A FastQC run will output the html report and output zip into output_path:

  • {input file name}_fastqc.html: FastQC HTML report for checking data quality
  • {input file name}\_fastqc.zip: Zip directory containing the HTML report and some supporting files

Tool Versions

Toolchest currently supports version 0.11.9 of FastQC.


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