Made snippet input- and output files more harmonised.

rnaseq/step1_fastqc/snippet.sh

@@ -1,5 +1,12 @@
-# The command to do a FastQC on a fastq file is
-file="file_to_analyse.fq.gz"
-fastqc_out="./path/to/fastqc/output/dir"
+#!/bin/bash
+R1="sample1_R1.fastq.gz"
+R2="sample1_R2.fastq.gz"
 
-fastqc -o "$fastqc_out" "$file"
+PROJECT_DIRECTORY="/groups/umcg-griac/tmp01/rawdata/$(whoami)/rnaseq"
+FASTQC_OUT="${PROJECT_DIRECTORY}/step1/"
+mkdir -p "${FASTQC_OUT}"
+
+# Run FastQC on paired-end data.
+fastqc \
+    -o "${FASTQC_OUT}" \
+    "${R1}" "${R2}"