Docker command line options
docker run
--rm
--name fastqc-ab
-u="$(id -u):$(id -g)"
-w="/data/"
-v ~/data/:/data
quay.io/biocontainers/fastqc:0.11.9--0
/bin/bash -c "fastqc WT*.fq.gz"Why do we use the following options?
| — rm | container removed after execution completed |
| -u | use user and group ID from the host |
| -w | use working directory in container |
| -v | mount data folder from host to container, file exchange |
| –name | own name of container |
From within the container, we run the bash command to be able to execute fastqc on all the files following the specified pattern.