fastqc-docker-singularity

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

FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.

Build docker container:

Not using Conda to keep image size small.

1. For FastQC installation instructions:

https://www.bioinformatics.babraham.ac.uk/projects/download.html#fastqc
See also: https://github.com/s-andrews/FastQC

2. Build the Docker Image

To build image from the command line:

# Assumes current working directory is the top-level fastqc-docker-singularity directory
docker build -t fastqc:0.11.9 . # tag should match software version

Can do this on Google shell

To test this tool from the command line:

docker run --rm -it fastqc:0.11.9 fastqc --help

# Optional: Run with test data from PICARD Test Data GCS bucket
# mkdir fastq_test && gsutil cp gs://gatk-test-data/wgs_fastq/NA12878_20k/H06HDADXX130110.1.ATCACGAT.20k_reads_1.fastq ./fastq_test/ && gzip fastq_test/*.fastq
docker run -it --rm -v "$PWD":/data -w /data fastqc:test2 fastqc fastq_test/H06HDADXX130110.1.ATCACGAT.20k_reads_1.fastq.gz --outdir=fastq_test
# -v mounts current working dir as /data in container
# -w sets working dir in conatiner
# SUCCESSFUL TEST RESULT: html reports and zip files of results in /fastq_test for 2x 10k reads

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 fastqc0.11.9-docker.tar && gzip fastqc0.11.9-docker.tar # = IMAGE_ID of fastqc image
docker run -v "$PWD":/data --rm -it singularity:1.1.5 bash -c "singularity build /data/fastqc0.11.9.sif docker-archive:///data/fastqc0.11.9-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 fastqc.sif file to the system on which you want to run FastQC from the Singularity container

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

# set up path to the FastQC Singularity container
FASTQC_SIF=path/to/fastqc.sif

# Test that FASTQC can run from Singularity container
singularity run $FASTQC_SIF fastqc --help # depending on system/version, singularity may be called apptainer

mattgalbraith/fastqc-docker-singularity