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 aFastQC_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
: 2memory
: 4GBcontainer
: ummidock/fastqcversion
: 0.11.7-1
trimmomatic
:cpus
: 2memory
: 4GB (dynamically increased on retry)container
: ummidock/trimmomaticversion
: 0.36-2
Advanced¶
Template¶
flowcraft.templates.fastqc_report
flowcraft.templates.trimmomatic
flowcraft.templates.trimmomatic_report
Reports JSON¶
tableRow
:Trimmed (%)
: Percentage of trimmed nucleotidesplotData
:sparkline
: Number of nucleotides after trimming
badReads
: Number of discarded reads