Cannot find ./bin scripts when running Nextflow with a container - nextflow

Question

I have a nextflow script that sources scripts located in the ./bin directory that is located where I invoke the nextflow script. When I run the workflow without a container, Nextflow can find these scripts and execute them. However, when I run Nextflow with a container the scripts cannot be found, despite that I attempted to add those scripts to the container file.
I guess that I am either not adding the executables to the container properly or that I am not referencing them properly in the Nextflow script or config file. Any help is appreciated.
Here is an example process:
process clean {
// Remove common contaminants from fastq(s) using tapioca script
// see: https://github.com/ncgr/tapioca
input:
path fastq_file from fastq_raw
val x from machine_name
output:
path 'out.fastq' into clean_out
stdout ch1
script:
"""
echo "Number of reads in $fastq_file"
grep -c "^#" $fastq_file
tap_contam_analysis --db ${dbdir}/phix174 --pct 80 ${fastq_file} > hits.txt
echo "PhiX filtering completed for ${fastq_file}"
"""
}
Note that the "tap_contam_analysis" script is a perl script located in ./bin from where I invoke the Nextflow script.
Here are the relevant parts of my Docker file. Note that I attempted to modify the $PATH in hopes that would fix the issue...no luck:
FROM ubuntu:18.04
ARG DEBIAN_FRONTEND=noninteractive
WORKDIR /usr/src
#Copy all the stuff for this Nextflow workflow (python and perl scripts)
COPY . .
ENV PATH=${PATH}:/usr/src/bin
Finally, here is my nextflow.config file:
process {
container = 'nf_se_demux_to_bam_bai_denovo'
}

Answer 1

The executables just need to be added to somewhere in your container's $PATH. Folks often like to use /usr/local/bin for this, but you can check other locations with:
docker run --rm ubuntu:18.04 bash -c 'echo $PATH'
Your Dockerfile, therefore, might look like this:
FROM ubuntu:18.04
ARG DEBIAN_FRONTEND=noninteractive
WORKDIR /usr/src
COPY ./bin /usr/local/bin