Hi All,
I am working to adapt a custom pipeline written with only using singularity in mind to being able to use docker as well. I didn’t make this pipeline but have used it before. I no longer have access to a computing environment with singularity available which is why I am trying to get it to work with docker.
This is the pipeline itself: GitHub - stenglein-lab/read_preprocessing: A nextflow workflow / pipeline to perform common NGS read preprocessing. This can be used as stand-alone or can be used as subworkflow in another nextflow pipeline.
I added this to the config file to add a docker profile:
docker { docker.enabled = true conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false docker.runOptions = ‘-u (id -u):(id -g)’ }
And looked at all the modules to see if they were already compatible with docker. To me, it looks like they all have a docker container option but I have been unable to find good documentation about setting up modules for multiple containers so this may be because of that. Any kind of direction to documentation about this would be incredibly helpful.
So, I ran the pipeline and at the third step it returned the error below. This has confounded me as it it’s a commonly used nf-cor module. What is the problem?
Caused by: K8s pod image cannot be pulled – rpc error: code = NotFound desc = failed to pull and unpack image “docker.io/biocontainers/fastqc:0.12.1--hdfd78af_0”: failed to unpack image on snapshotter overlayfs: unexpected media type text/html for sha256:62767d3a9e5db738ab69e115188c8e61b80ff4eb7ba70c083b2e766fe15e92e4: not found
Command executed:
printf “%s %s\n” 12-P0104-02-22_S1_R1_001.fastq.gz 12-P0104-02-22_1.gz 12-P0104-02-22_S1_R2_001.fastq.gz 12-P0104-02-22_2.gz | while read old_name new_name; do
[ -f “${new_name}” ] || ln -s $old_name $new_name
done
fastqc
–threads 6
12-P0104-02-22_1.gz 12-P0104-02-22_2.gz
cat <<-END_VERSIONS > versions.yml
“MAIN_WORKFLOW:PREPROCESS_READS:FASTQC_PRE”:
fastqc: $( fastqc --version | sed -e “s/FastQC v//g” )
END_VERSIONS
Thank you!