Fastqc_trimmomatic

Purpose

This component runs Trimmomatic on paired-end FastQ files but uses information on the per-base GC content variation reported by FastQC to guide the trimming of the FastQ reads.

Note

Software pages: FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/); Trimmoatic (http://www.usadellab.org/cms/?page=trimmomatic)

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 used to screen overrepresented sequences against and to filter the FastQ files.
  • trimSlidingWindow: Perform sliding window trimming, cutting once the average quality within the window falls below a threshold.
  • trimLeading: Cut bases off the start of a read, if below a threshold quality.
  • trimTrailing: Cut bases of the end of a read, if below a threshold quality.
  • trimMinLength: Drop the read if it is below a specified length.

Published results

  • results/trimmomatic: The trimmed FastQ files for each sample.

Published reports

  • reports/fastqc: Stores the FastQC HTML reports for each sample and a FastQC_trim_report.csv file containing the trimming values suggested by the analysis of the FastQC report.
  • reports/fastqc/run_1/: Stores the summary text files with the category results of FastQC for each sample.

Default directives

  • fastqc:
    • cpus: 2
    • memory: 4GB
    • container: ummidock/fastqc
    • version: 0.11.7-1
  • trimmomatic:
    • cpus: 2
    • memory: 4GB (dynamically increased on retry)
    • container: ummidock/trimmomatic
    • version: 0.36-2

Advanced

Reports JSON

tableRow:
Trimmed (%): Percentage of trimmed nucleotides
plotData:
sparkline: Number of nucleotides after trimming

badReads: Number of discarded reads