jysgro/fastqc repository overview

fastqc 12.1 under Ubuntu 23.04

Based on pegi3s/fastqc/⁠ updated from Ubuntu 19.04 to 23.04 and fastqc version 11.9 to 12.1. Based on their Docker⁠ file (See below.)

Note: There is an entry point: If used by supplying one or more FastQ or gzip version it works fine, or even the wild card *. If no filename is provided then fastqc will start the GUI and will fail in most cases and complain about X11. (Learn more about Entrypoint⁠.)

The following command is formatted to work on Macintosh (bash or zsh), Linux (bash), and Windows PowerShell by using ${PWD}:

docker run -it --rm -v ${PWD}:/data -w /data pegi3s/fastqc:0.12.1 * 

The container will be interactive (-it), deleted when job is finshed (--rm), share the current directory (${PWD}), mapped as /data, and set the working directory as /data. The wild card * will find all files within the directory. Or a list of desired files can be provided.

Using the recompiled version:

docker run -it --rm -v ${PWD}:/data -w /data jysgro/fastqc:ub2306_12.1  *