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
: 2memory
: 4GBcontainer
: ummidock/fastqcversion
: 0.11.7-1
Advanced¶
Template¶
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 database_gc_content
: GC content distributionbase_n_content
: Per base N contentsequence_length_dist
: Distribution of sequence read lengthper_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.