trimmomatic¶
Purpose¶
This component runs Trimmomatic on paired-end FastQ files.
Note
Software page: 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 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.reports/fastqc/run_2/
: Stores the summary text files with the category results of FastQC for each sample.
Default directives¶
cpus
: 2memory
: 4GB (dynamically increased on retry)container
: ummidock/trimmomaticversion
: 0.36-2