Answers.Body: <p>It's a good idea to pass around structured metadata, but together with data/files, as tuples: tutorial <a href="https://training.nextflow.io/advanced/metadata/" rel="nofollow noreferrer">here</a></p>
  <p>So, like this:</p>
  <pre><code>process bamToFastq {
      input:
          tuple val(meta), path(bam)
  
      container 'quay.io/biocontainers/samtools:1.8--4'
      cpus 4
      disk '50 GB'
  
      output:
          tuple val(meta), file('r0.fastq'), emit: read_other
          tuple val(meta), file('r{1,2}.fastq'), emit: read_paired
      &quot;&quot;&quot;
      samtools fastq -0 r0.fastq -1 r1.fastq -2 r2.fastq -@ <span class="math-container">${task.cpus} $</span>bam
      &quot;&quot;&quot;
  }
  </code></pre>
  <p>If you need to update/carry over URLs/other metadata, I recommend doing this outside of processes - using <code>map</code> constructs on channel outputs.</p>
  
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Body: <p>I have a number of samples (from the 1000 genomes) that I want to analyse using Nextflow. However, I need to keep track of their metadata, fields like sample ID, analysis type etc. So I have a basic metadata object like this for each sample that I then pipe into a channel:</p>
  
  <pre><code>            metadata = [
                  sample: split[0],
                  mapped: split[1],
                  platform : split[2],
                  alignment: split[3],
                  tsi: split[4],
                  type: split[5],
                  date: split[6],
                  filetype: split[7..-1],
                  url: file(bam)
              ]
  </code></pre>
  
  <p>Then, in the first process, I attempt to use this metadata object:</p>
  
  <pre><code>process bamToFastq {
      input:
          val bam
  
      container 'quay.io/biocontainers/samtools:1.8--4'
      cpus 4
      disk '50 GB'
  
      output:
          file('r*.fastq') into fastq
  
      """
      samtools fastq -0 r0.fastq -1 r1.fastq -2 r2.fastq -@ <span class="math-container">${task.cpus} $</span>bam.url
      """
  }
  </code></pre>
  
  <p>However, I already run into some issues:</p>
  
  <ul>
  <li>Nextflow doesn't realise that <code>metadata.url</code> is a file, since I declared the whole object using <code>val</code>, so I'm guessing it won't be correctly localized (based on <a href="https://www.nextflow.io/docs/latest/process.html#input-of-files" rel="nofollow noreferrer">the documentation</a>).</li>
  <li>I want pass down a new metadata object for each of my generated FASTQs, that's the same as the input one, but I want to add in the FASTQ as a URL, and the read number of each FASTQ. Where/how can I do this? Nextflow doesn't provide any section of the <code>process</code> for structuring the output data. If this were Python I would do the following:</li>
  </ul>
  
  <pre class="lang-py prettyprint-override"><code>    metadata = bam.copy()
      metadata['fastq'] = file
      metadata['read_number'] = file.name[1]
  </code></pre>
  
  <p>Is there a good way to pass around structured metadata like this in nextflow? Will this solve either of my problems?</p>
  
Tags: <nextflow>
Title: Passing around complex metadata in Nextflow
ThreadText: # Passing around complex metadata in Nextflow
  
  (Asked by: username_0 on 2019-07-30)
  
  I have a number of samples (from the 1000 genomes) that I want to analyse using Nextflow. However, I need to keep track of their metadata, fields like sample ID, analysis type etc. So I have a basic metadata object like this for each sample that I then pipe into a channel:
  
  ```
              metadata = [
                  sample: split[0],
                  mapped: split[1],
                  platform : split[2],
                  alignment: split[3],
                  tsi: split[4],
                  type: split[5],
                  date: split[6],
                  filetype: split[7..-1],
                  url: file(bam)
              ]
  
  ```
  
  Then, in the first process, I attempt to use this metadata object:
  
  ```
  process bamToFastq {
      input:
          val bam
  
      container 'quay.io/biocontainers/samtools:1.8--4'
      cpus 4
      disk '50 GB'
  
      output:
          file('r*.fastq') into fastq
  
      """
      samtools fastq -0 r0.fastq -1 r1.fastq -2 r2.fastq -@ ${task.cpus} $bam.url
      """
  }
  
  ```
  
  However, I already run into some issues:
  
  * Nextflow doesn't realise that `metadata.url` is a file, since I declared the whole object using `val`, so I'm guessing it won't be correctly localized (based on [the documentation](https://www.nextflow.io/docs/latest/process.html#input-of-files)).
  * I want pass down a new metadata object for each of my generated FASTQs, that's the same as the input one, but I want to add in the FASTQ as a URL, and the read number of each FASTQ. Where/how can I do this? Nextflow doesn't provide any section of the `process` for structuring the output data. If this were Python I would do the following:
  
  ```py
      metadata = bam.copy()
      metadata['fastq'] = file
      metadata['read_number'] = file.name[1]
  
  ```
  
  Is there a good way to pass around structured metadata like this in nextflow? Will this solve either of my problems?
  
  **Tags:** nextflow
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-08-26. Score: 0
  
  It's a good idea to pass around structured metadata, but together with data/files, as tuples: tutorial [here](https://training.nextflow.io/advanced/metadata/)
  
  So, like this:
  
  ```
  process bamToFastq {
      input:
          tuple val(meta), path(bam)
  
      container 'quay.io/biocontainers/samtools:1.8--4'
      cpus 4
      disk '50 GB'
  
      output:
          tuple val(meta), file('r0.fastq'), emit: read_other
          tuple val(meta), file('r{1,2}.fastq'), emit: read_paired
      """
      samtools fastq -0 r0.fastq -1 r1.fastq -2 r2.fastq -@ ${task.cpus} $bam
      """
  }
  
  ```
  
  If you need to update/carry over URLs/other metadata, I recommend doing this outside of processes - using `map` constructs on channel outputs.
  
  
  ---
  
  