Fastqc¶

Generate fastq qc statistics using fastqc.

Software dependencies¶

fontconfig ==2.12.1
fastqc ==0.11.5

Example¶

rule fastqc:
  input:
    "raw/{sample.fastq}" # A fastq file
  output:
    html = "fastqc/{sample}.html", # HTML file containing statistics
    zip = "fastqc/{sample}.zip" # Zip file containing statistics
  wrapper:
    "fastqc"

Usage¶

Run snakemake with

snakemake --wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/

to automatically download the wrapper fastqc and include it in the snakefile.

Note that input, output and log file paths can be chosen freely. When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Authors¶

Julian de Ruiter