---
title: "fastqc"
output: html_document
---


# Directories and programs

fastqc="/home/shared/FastQC/fastqc"

```{bash}

#FastQC 

fastqc="/home/shared/FastQC/fastqc"

#Populate array with FastQ files
fastq_array=(/home/shared/8TB_HDD_01/sr320/ncbi/*.fastq)

#Pass array contents to new variable
fastqc_list=$(echo "${fastq_array[*]}")

#Run FastQC
${fastqc} \
--threads 28 \
${fastqc_list} \
-o /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/fastqc01 \
2>&1 | tee /home/shared/8TB_HDD_01/sr320/github/nb-2022/P_generosa/analyses/fastqc01/stdout
```

