fastqc

Purpose

This components runs FastQC on paired-end FastQ files.

Note

Software page: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Input/Output type

  • Input type: FastQ
  • Output type: FastQ

Note

The default input parameter for FastQ data is --fastq. You can change the --fastq parameter default pattern (fastq/*_{1,2}.*) according to input file names (e.g.: --fastq "path/to/fastq/*R{1,2}.*").

Parameters

  • adapters: Provide a non-default fasta file containing the adapter sequences to screen overrepresented sequences against.

Published results

None.

Published reports

  • reports/fastqc: Stores the FastQC HTML reports for each sample.
  • reports/fastqc/run_2/: Stores the summary text files with the category results of FastQC for each sample.

Default directives

  • cpus: 2
  • memory: 4GB
  • container: ummidock/fastqc
  • version: 0.11.7-1

Advanced

Reports JSON

plotData:
  • base_sequence_quality: Per base sequence quality data
    • (This structure is repeated for the other entries)
    • status: Status of the category (PASS, WARN, etc)
    • data: Plot data
  • sequence_quality: Per sequence quality data
  • base_gc_content: GC content distribution
  • base_n_content: Per base N content
  • sequence_length_dist: Distribution of sequence read length
  • per_base_sequence_content: Per base sequence content
warnings:
  • List of failures or warnings for some non-sensitive FastQC categories
fail:
  • Failure message when sensitive FastQC categories fail or do not pass.