docker-fastqc

The current version of this pipeline pulls the Docker image from a public AWS Elastic Container Registry. If you prefer to pull from Docker Hub (DH), please use the tagged version utilizing DH: v2_DH.

This repo contains the source files for a docker image stored in both 4dndcic/fastqc:v2 and AWS public.ecr.aws/dcic-4dn/fastqc:v2.

Table of contents

• Cloning the repo
• Tool specifications
• Building docker image
• Benchmarking tools
• Sample data
• Tool wrappers
  • run.sh

Cloning the repo

git clone https://github.com/4dn-dcic/docker-fastqc
cd docker-fastqc

Tool specifications

Major software tools used inside the docker container are downloaded by the script downloads.sh. This script also creates a symlink to a version-independent folder for each software tool. In order to build an updated docker image with a new version of the tools, ideally only downloads.sh should be modified, but not Dockerfile, unless the new tool requires a specific APT tool that need to be downloaded. The downloads.sh file also contains comment lines that specifies the name and version of individual software tools.

Building docker image

You need docker daemon to rebuild the docker image. If you want to push it to a different docker repo, replace 4dndcic/fastqc:v2 with your desired docker repo name. You need permission to push to 4dndcic/fastqc:v2.

docker build -t 4dndcic/fastqc:v2 .
docker push 4dndcic/fastqc:v2

You can skip this if you want to use an already built image on docker hub (image name 4dndcic/fastqc:v2). The command 'docker run' (below) automatically pulls the image from docker hub.

Benchmarking tools

To obtain run time and max mem stats, use usr/bin/time that is installed in the docker container. For example, run the following to benchmark du.

docker run 4dndcic/fastqc:v2 /usr/bin/time du 2> log
cat log

The output looks as follows:

0.02user 0.82system 0:00.87elapsed 96%CPU (0avgtext+0avgdata 2024maxresident)k
0inputs+0outputs (0major+103minor)pagefaults 0swaps

The benchmarking result goes to STDERR, which can be collected by a file by redirecting with 2>. Maxmem is 2024KB in this case ('maxresident'). Run time is 0.87 second. ('elapsed')

Sample data

Sample data files that can be used for testing the tools are included in the sample_data folder. These data are not included in the docker image.

Tool wrappers

Tool wrappers are under the scripts directory and follow naming conventions run*.sh. These wrappers are copied to the docker image at built time and may be used as a single step in a workflow.

# default
docker run 4dndcic/fastqc:v2

# specific run command
docker run 4dndcic/fastqc:v2 <run_script> <arg1> <arg2> ...

# may need -v option to mount data file/folder if they are used as arguments.
docker run -v /data1/:/d1/:rw -v /data2/:/d2/:rw 4dndcic/fastqc:v2 <run_script> /d1/file1 /d2/file2 ...

run.sh

Runs fastqc on a given fastq(.gz) file and produces a fastqc report.

• Input: a fastq file (either gzipped or not)
• Output: a fastqc report (data_report.zip)

Usage

Run the following in the container

run.sh <input_fastq> <nthread> <outdir>
# input_fastq : an input fastq file, either gzipped or not.
# nthread : number of threads to use
# outdir : output directory (This should be a mounted host directory, so that the output files are visible from the host and to avoid any bus error)