Fastqc - Html Summary For Joined Reads

Aggregate quality control results from all FastQC reports and generate summary HTML table with PASS/WARN/FAIL icons

Location

• Filepath: <SnakeLines_dir>/rules/single_end/reads/report/quality_report/fastqc.snake
• Rule name: fastqc__html_summary_for_joined_reads

Input(s):

• fastq_files: All joined Fastq files to quality report

Output(s):

• summary: HTML report with summary statistics of multiple fastq files

Fastqc - Html Summary For Paired Reads

Aggregate quality control results from all FastQC reports and generate summary HTML table with PASS/WARN/FAIL icons

Location

• Filepath: <SnakeLines_dir>/rules/single_end/reads/report/quality_report/fastqc.snake
• Rule name: fastqc__html_summary_for_paired_reads

Input(s):

• fastq_files: All Fastq files to quality report

Output(s):

• summary: HTML report with summary statistics of multiple fastq files

Fastqc - Quality Report

Generate HTML report with plots assessing various quality control aspects of NGS reads

Location

• Filepath: <SnakeLines_dir>/rules/single_end/reads/report/quality_report/fastqc.snake
• Rule name: fastqc__quality_report

Input(s):

• reads: Sequenced reads in fastq format

Output(s):

• html: Quality report in HTML format
• txt: Quality report in text format suitable for automated processing