4.6 Example execution:

Using the 2 fastqc available files, process them outside and inside the mounted directory.

Let’s use our fastqc.sif image file and we place it in $HOME

# Let's create a dummy directory
mkdir $HOME/scratch

# Let's copy contents of testdata in scratch

singularity exec fastqc.sif fastqc scratch/*fastq.gz

# Check you have some HTMLs there. Remove them
rm scratch/*html

# Let's use shell
singularity shell fastqc.sif
> cd scratch
> fastqc *fastq.gz
> exit

# Check you have some HTMLs there. Remove them
singularity exec -B ./scratch:/fastqcdir fastqc.sif fastqc /fastqcdir/*fastq.gz

# What happens here!
singularity exec -B ./scratch:/fastqcdir fastqc.sif bash -c 'fastqc /fastqcdir/*fastq.gz'