text: user16328: 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.
  
  user10775: 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"
  
  
original_text: 16328: <p>I'm using the following script to detect strandedness of my paired end RNA-seq data.</p>
  <pre><code>#!/usr/bin/env bash
  
  cd ~/Desktop/fastq
  
  for infile in *_1.fastq
  do
     base=<span class="math-container">$(basename $</span>{infile} _1.fastq)
  
      docker run quay.io/biocontainers/guessmylt:0.2.5--py_0 GUESSmyLT \
      --reads <span class="math-container">${infile} $</span>{base}_2.fastq
  
  done
  </code></pre>
  <p>But when I run it, it keeps giving the error:</p>
  <pre><code>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
  </code></pre>
  <p>Why is it appending double '/' to the fastq file's path? Nowhere in my script did I mention any path.</p>
  <p><em>I apologize for the very vague title, English is not my first language, so I did not know how else to phrase it.</em></p>
   10775: <p>The issue here is that the current working directory inside the container is <code>/</code>. You can see this with:</p>
  <pre><code>docker run --rm quay.io/biocontainers/guessmylt:0.2.5--py_0 python \
      -c 'import os; print(os.getcwd())'
  </code></pre>
  <p>When <a href="https://github.com/NBISweden/GUESSmyLT" rel="nofollow noreferrer">GUESSmyLT</a> tries to get the absolute path of it's arguments (<code>--reads</code>, <code>--reference</code>, <code>--output</code>, etc), it actually appends a trailing slash to the current working directory<sup><a href="https://github.com/NBISweden/GUESSmyLT/blob/v1.0/GUESSmyLT/GUESSmyLT.py#L21" rel="nofollow noreferrer">1</a></sup>, hence the double slash in the returned file names.</p>
  <p>To pass the files into the container and ensure that the results are available when it exits, you'll need a <a href="https://docs.docker.com/engine/reference/run/#volume-shared-filesystems" rel="nofollow noreferrer">volume</a> mount anyway. For example:</p>
  <pre><code>docker run --rm -v &quot;${PWD}:/working&quot; quay.io/biocontainers/guessmylt:0.2.5--py_0 GUESSmyLT \
      --reads &quot;/working/${base}_1.fastq&quot; &quot;/working/${base}_2.fastq&quot; \
      --reference &quot;/working/reference.fa&quot; \
      --annotation &quot;/working/annotation.gtf&quot; \
      --output &quot;/working&quot;
  </code></pre>
  