How to remove double '/' from file path, bash script

Question

I'm using the following script to detect strandedness of my paired end RNA-seq data.

#!/usr/bin/env bash

cd ~/Desktop/fastq

for infile in *_1.fastq
do
   base=$(basename ${infile} _1.fastq)

    docker run quay.io/biocontainers/guessmylt:0.2.5--py_0 GUESSmyLT \
    --reads ${infile} ${base}_2.fastq

done

But when I run it, it keeps giving the error:

Building DAG of jobs... File path //SRR3475890_1.fastq contains double
'/'. This is likely unintended. It can also lead to inconsistent
results of the file-matching approach used by Snakemake. File path
//SRR3475890_2.fastq contains double '/'. This is likely unintended.
It can also lead to inconsistent results of the file-matching approach
used by Snakemake. MissingInputException in line 46 of
/usr/local/lib/python3.6/site-packages/GUESSmyLT/subsample: Missing
input files for rule subsample_fastq: //SRR3475890_2.fastq
//SRR3475890_1.fastq

Why is it appending double '/' to the fastq file's path? Nowhere in my script did I mention any path.

I apologize for the very vague title, English is not my first language, so I did not know how else to phrase it.

Answer 1

The issue here is that the current working directory inside the container is /. You can see this with:

docker run --rm quay.io/biocontainers/guessmylt:0.2.5--py_0 python \
    -c 'import os; print(os.getcwd())'

When GUESSmyLT tries to get the absolute path of it's arguments (--reads, --reference, --output, etc), it actually appends a trailing slash to the current working directory¹, hence the double slash in the returned file names.

To pass the files into the container and ensure that the results are available when it exits, you'll need a volume mount anyway. For example:

docker run --rm -v "${PWD}:/working" quay.io/biocontainers/guessmylt:0.2.5--py_0 GUESSmyLT \
    --reads "/working/${base}_1.fastq" "/working/${base}_2.fastq" \
    --reference "/working/reference.fa" \
    --annotation "/working/annotation.gtf" \
    --output "/working"