Answers.Body: <p>I discovered a solution using a combination of <code>.collect()</code> and <code>each</code>.</p>
  <p>If one collects from a path the result is a value channel of paths. Value channels can be used multiple times, whereas queue channels cannot.</p>
  <pre><code>ch_collected = Channel.fromPath( &quot;somepath&quot; ).collect()
  </code></pre>
  <p><code>ch_collected</code> can be used multiple times but if one tries to input it to a process using the usual file..from syntax one will get all the files input to the process at once. Instead, one must use the <code>each</code> option during input. E.g.,</p>
  <pre><code>  input:
      each fastq_file from ch_collected
  </code></pre>
  <p>I hope this helps someone.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
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Answers.Text: Thanks for answering your own quesiton :-).
Answers.UserDisplayName: Kamil S Jaron
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Answers.LastEditDate: 2022-01-13T23:39:41.467Z
Answers.UserDisplayName: jh_
Answers.Body: <p>Use a value channel:</p>
  <pre><code>exampleChannel_onething = Channel.value(1)
  </code></pre>
  <p>On existing channels, you can use <a href="https://www.nextflow.io/docs/latest/operator.html#first" rel="nofollow noreferrer">https://www.nextflow.io/docs/latest/operator.html#first</a> (or similar) to convert to a value channel.</p>
  
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Answers.UserDisplayName: Rolf
Body: <p>I am trying to find a hack for getting a process to run until all emissions in a channel are used up. The problem is that the process also takes as input a second channel that only has a single emission. Therefore, the process only runs once, but I need it to repeatedly use the single emission channel for all the emissions in the other channel. I imagine this is not too uncommon a problem, but I have not found a solution.</p>
  <p>To be more clear, here is the actual bioinformatics I am trying to do: I have split fastqs into files for multiple samples and emit these files into a channel. I copy this channel because I want to use the files again later. I then build an assembly from the combined files which I index with bwa. I next pass the indexed assembly (index channel) into a new process that also takes as input ALL of the original fastq files (the ones I put into a duplicate channel earlier). The goal is to align each of the fastq files against the genome. However, there are only a few emissions in the index channel so the process doesn't repeat for all the items in my fastq channel.</p>
  <p>To aid you all here is a simple example that may help, but take note that my situation doesn't use value channels so is a bit trickier to deal with.</p>
  <pre><code>exampleChannel_multiplethings = Channel.from( [1, 3, 5, 7, 9] )
  exampleChannel_onething = Channel.from( [1] )
  
  process foo {
    input:
    val x from exampleChannel_multiplethings
    val y from exampleChannel_onething
    
    output:
    file 'x.txt' into foo_out
  
    &quot;&quot;&quot;
    echo <span class="math-container">$y $</span>x &gt; x.txt
    &quot;&quot;&quot;
  }
  </code></pre>
  <p>This outputs &quot;1 1&quot; into the x.txt file. This is expected behavior, but I need to circumvent it somehow so that the process is repeated for all the items in the exampleChannel_multiplethings channel. Important note, if I was dealing with single values I could probably use one of the combine operators, but in reality I am trying to pass a handful of files for an indexed genome into the process. I haven't found a combine operator that works, but hopefully I have missed something!</p>
  <p>Thanks for any assistance</p>
  <p>Actual code (overly lengthy to paste here) can be found at: <a href="https://github.com/JHarrisonEcoEvo/nextflow_gbs/blob/main/gbs_nextflow" rel="nofollow noreferrer">https://github.com/JHarrisonEcoEvo/nextflow_gbs/blob/main/gbs_nextflow</a></p>
  
Tags: <bwa><nextflow>
Title: How fo force nextflow to repeat a process until all values in a particular channels are used up BUT a single value from another channel is needed
ThreadText: # How fo force nextflow to repeat a process until all values in a particular channels are used up BUT a single value from another channel is needed
  
  (Asked by: username_0 on 2022-01-13)
  
  I am trying to find a hack for getting a process to run until all emissions in a channel are used up. The problem is that the process also takes as input a second channel that only has a single emission. Therefore, the process only runs once, but I need it to repeatedly use the single emission channel for all the emissions in the other channel. I imagine this is not too uncommon a problem, but I have not found a solution.
  
  To be more clear, here is the actual bioinformatics I am trying to do: I have split fastqs into files for multiple samples and emit these files into a channel. I copy this channel because I want to use the files again later. I then build an assembly from the combined files which I index with bwa. I next pass the indexed assembly (index channel) into a new process that also takes as input ALL of the original fastq files (the ones I put into a duplicate channel earlier). The goal is to align each of the fastq files against the genome. However, there are only a few emissions in the index channel so the process doesn't repeat for all the items in my fastq channel.
  
  To aid you all here is a simple example that may help, but take note that my situation doesn't use value channels so is a bit trickier to deal with.
  
  ```
  exampleChannel_multiplethings = Channel.from( [1, 3, 5, 7, 9] )
  exampleChannel_onething = Channel.from( [1] )
  
  process foo {
    input:
    val x from exampleChannel_multiplethings
    val y from exampleChannel_onething
    
    output:
    file 'x.txt' into foo_out
  
    """
    echo $y $x > x.txt
    """
  }
  
  ```
  
  This outputs "1 1" into the x.txt file. This is expected behavior, but I need to circumvent it somehow so that the process is repeated for all the items in the exampleChannel\_multiplethings channel. Important note, if I was dealing with single values I could probably use one of the combine operators, but in reality I am trying to pass a handful of files for an indexed genome into the process. I haven't found a combine operator that works, but hopefully I have missed something!
  
  Thanks for any assistance
  
  Actual code (overly lengthy to paste here) can be found at: <https://github.com/JHarrisonEcoEvo/nextflow_gbs/blob/main/gbs_nextflow>
  
  **Tags:** bwa, nextflow
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2022-01-13. Score: 5
  
  I discovered a solution using a combination of `.collect()` and `each`.
  
  If one collects from a path the result is a value channel of paths. Value channels can be used multiple times, whereas queue channels cannot.
  
  ```
  ch_collected = Channel.fromPath( "somepath" ).collect()
  
  ```
  
  `ch_collected` can be used multiple times but if one tries to input it to a process using the usual file..from syntax one will get all the files input to the process at once. Instead, one must use the `each` option during input. E.g.,
  
  ```
    input:
      each fastq_file from ch_collected
  
  ```
  
  I hope this helps someone.
  
  > **Comments:**
  > **username_1**: Thanks for answering your own quesiton :-).  
  
  ---
  
  ### Answer by username_2 on 2024-05-31. Score: 2
  
  Use a value channel:
  
  ```
  exampleChannel_onething = Channel.value(1)
  
  ```
  
  On existing channels, you can use <https://www.nextflow.io/docs/latest/operator.html#first> (or similar) to convert to a value channel.
  
  
  ---
  
  