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

Function Call


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.

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}\ Zip directory containing the HTML report and some supporting files

Tool Versions

Toolchest currently supports version 0.11.9 of FastQC.