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

Function Call

tc.fastqc(
    inputs,
    output_path=None,
    contaminants=None,
    adapters=None,
    limits=None,
    tool_args="",
    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. \nSAM, BAM, or FASTQ formats are supported, as well as gzip-compressed variants. The files can be a local or remote, see Using Files.
`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 Using Files.
`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.

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

Toolchest currently supports version 0.11.9 of FastQC.