fastqscreen-docker-singularity

Build Docker container for FastQ Screen software and (optionally) convert to Apptainer/Singularity.

FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.

Requirements:

Perl
Bowtie, Bowtie2 (default) or BWA
wget (optional - required for --get_genomes)
gzip (optional - required for reading gzipped FASTQ files?)
SAMtools (optional) # not currently included in image
GD::Graph (optional - required for png output) # not currently included in image
Bismark (bisulfite mapping only) # not currently included in image
Reference genome indices
fastq_screen.conf file with reference info (will keep outside container and pass with --conf)
Test Dataset (optional)

Build docker container:

Not using Conda so we can keep image size small.

1. For FastQ Screen installation instructions:

https://stevenwingett.github.io/FastQ-Screen/
See also: https://github.com/StevenWingett/FastQ-Screen

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level fastqscreen-docker-singularity directory
docker build -t fastqscreen:0.15.2 . # tag should match software version

• Can do this on Google shell

To test this tool from the command line:

docker run --rm -it fastqscreen:0.15.2 fastq_screen --help

Obtaining reference genomes

Download pre-built Bowtie2 indices of commonly used genomes downloaded directly from the Babraham Bioinformatics website and add to fastq_screen.conf file (see next)

docker run -it --rm -v ${PWD}:/data -w /data fastq_screen:test fastq_screen --get_genomes --outdir /data/References

Alternatively, use existing genome indices or build for aligner(s) of choice from FASTA files according to aligner instructions and add to fastq_screen.conf file (see next)

Set up fastq_screen.conf file

By default the program looks for a configuration file named “fastq_screen.conf” in the folder where the FastQ Screen script it is located. If you wish to specify a different configuration file, which may be placed in a different folder (or outside your container), then use the --conf option.
Edit the file to add the correct paths to each genome index (Note: only the basename of the index files is required).

Example if mounted in container at /references as shown below:

#########
## Human - sequences available from
## ftp://ftp.ensembl.org/pub/current/fasta/homo_sapiens/dna/
DATABASE	Human	/references/Human/Homo_sapiens.GRCh38

#########
## Mouse - sequence available from
## ftp://ftp.ensembl.org/pub/current/fasta/mus_musculus/dna/
DATABASE	Mouse	/references/Mouse/Mus_musculus.GRCm38

Run with test data

wget https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/fastq_screen_test_dataset.tar.gz && tar -xzvf fastq_screen_test_dataset.tar.gz

REFERENCES_DIR=/path/to/references # location on host system

docker run -it --rm -v ${PWD}:/data -w /data -v ${REFERENCES_DIR}:/references fastqscreen:0.15.2 \
	fastq_screen \
	--conf ./fastq_screen.conf \
	./fastq_screen_test_dataset/fqs_test_dataset.fastq.gz \
	--outdir /data/test_results
# -v ${PWD}:/data mounts current working dir as /data in container
# -w /data sets working dir in container
# -v ${REFERENCES_DIR}:/references mounts REFERENCES_DIR as /references in container

# SUCCESSFUL TEST RESULT: html, txt, png files with results similar to those provided in the tast data archive

Optional: Conversion of Docker image to Singularity

3. Build a Docker image to run Singularity

(skip if this image is already on your system)
https://github.com/mattgalbraith/singularity-docker

4. Save Docker image as tar and convert to sif (using singularity run from Docker container)

docker images
docker save <Image_ID> -o fastqscreen0.15.2-docker.tar && gzip fastqscreen0.15.2-docker.tar # = IMAGE_ID of fastqscreen image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/fastqscreen0.15.2.sif docker-archive:///data/fastqscreen0.15.2-docker.tar.gz"

NB: On Apple M1/M2 machines ensure Singularity image is built with x86_64 architecture or sif may get built with arm64

Next, transfer the fastqscreen.sif file to the system on which you want to run FastQ Screen from the Singularity container

5. Test singularity container on (HPC) system with Singularity/Apptainer available

# set up path to the FastQ Screen Singularity container
FASTQ_SCREEN_SIF=path/to/fastqscreen0.15.2.sif

# Test that FastQ Screen can run from Singularity container
singularity run $FASTQ_SCREEN_SIF fastq_screen --help # depending on system/version, singularity may be called apptainer