Answers.Body: <p>There are many ways to accomplish this. Assuming you don't need to process single-end and paired-end reads simultaneously (i.e. within the same run), one way using the <a href="https://www.nextflow.io/docs/latest/channel.html#fromfilepairs" rel="nofollow noreferrer"><code>fromFilePairs</code></a> factory method is to just use an additional flag to define the number of files each emitted item is expected to hold. And then adjust your process definition accordingly:</p>
  <pre><code>params.reads = &quot;${projectDir}/data/*_{1,2}.fastq.gz&quot;
  params.singleEnd = false
  
  
  process TRIM {
  
      tag &quot;${pair_id}&quot;
  
      cpus 1
  
      input:
      tuple val(pair_id), path(reads)
  
      output:
      tuple val(pair_id), path(&quot;${pair_id}/*.atria.fastq{,.gz}&quot;)
  
      script:
      def single = reads instanceof Path
  
      def read1 = !single ? /-r &quot;<span class="math-container">${reads[0]}"/ : /-r "$</span>{reads}&quot;/
      def read2 = !single ? /-R &quot;${reads[1]}&quot;/ : ''
  
      &quot;&quot;&quot;
      atria \\
          -t <span class="math-container">${task.cpus} \\
          $</span>{read1} \\
          <span class="math-container">${read2} \\
          -l 12 \\
          -q 30 \\
          -o "$</span>{pair_id}&quot;
      &quot;&quot;&quot;
  }
  </code></pre>
  <pre><code>workflow {
  
      Channel
          .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
          .ifEmpty { error &quot;Could not find any reads matching pattern: ${params.reads}&quot; }
          .set { reads }
  
      TRIM( reads ).view()
  }
  </code></pre>
  <p>Although we've used an additional flag, it does let the pipeline fail immediately if it can't find the files it expects. I think this approach is more explicit and provides a better user experience:</p>
  <pre><code>$ nextflow run main.nf --reads './data/*.fastq'
  N E X T F L O W  ~  version 22.10.0
  Launching `main.nf` [nasty_allen] DSL2 - revision: 2cbc311974
  Could not find any reads matching pattern: ./data/*.fastq
  
   -- Check script 'main.nf' at line: 38 or see '.nextflow.log' file for more details
  </code></pre>
  <p>Doh! I forgot that these are single ended reads:</p>
  <pre><code>$ nextflow run main.nf --reads './data/*.fastq' --singleEnd
  N E X T F L O W  ~  version 22.10.0
  Launching `main.nf` [clever_gutenberg] DSL2 - revision: 2cbc311974
  executor &gt;  local (3)
  [8e/f90c90] process &gt; TRIM (X) [100%] 3 of 3 ✔
  [Y, /path/to/work/e6/48df1485bb7de8355ed8ce0f1b53da/Y/Y.atria.fastq]
  [Z, /path/to/work/eb/aca3389344ac03ff283ded0c46a7a6/Z/Z.atria.fastq]
  [X, /path/to/work/8e/f90c90210103c03a3fbde697e01227/X/X.atria.fastq]
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-12-22T14:22:38.737Z
Answers.LastActivityDate: 2022-12-22T14:22:38.737Z
Answers.UserDisplayName: Steve
Answers.Body: <p>My personal strategy is to always read data from a samplesheet which then auto-detects whether a sample is paired-end or single-end and stores this information in a so-called meta map (inspired by nf-core) which then passes this information to the modules.</p>
  <p>Example:</p>
  <p>Say you have a samplesheet that is a three-column csv file with a header:</p>
  <pre><code>$ cat samplesheet.csv 
  sample,r1,r2
  sample1,/Users/atpoint/sample1_R1.fq.gz,/Users/atpoint/sample1_R2.fq.gz
  sample2,/Users/atpoint/sample2_R1.fq.gz,
  </code></pre>
  <p>Read this into Nextflow and detect whether r2 has an entry. If so it is paired-end, else it is single-end:</p>
  <pre><code>
  # main.nf
  
  nextflow.enable.dsl = 2
  
  // Channel for the samplesheet
  ch_samplesheet = Channel.fromPath(&quot;/Users/atpoint/samplesheet.csv&quot;)
  
  // Parse it line by line
  ch_reads = ch_samplesheet.splitCsv(header:true).map {
  
      // This is the read1 and read2 entry
      r1 = it['r1']
      r2 = it['r2']
  
      // Detect wiether single-end or paired-end
      is_singleEnd = r2.toString()=='' ? true : false
      
      // The &quot;meta&quot; map, which is a Nextflow/Groovy map with id (the sample name) and a single_end logical entry
      meta = [id: it['sample'], single_end: is_singleEnd]
      
      // We return a nested map, the first entry is the meta map, the second one is the read(s)
      r2.toString()=='' ? [meta, [r1]] : [meta, [r1, r2]]
  
  }
  
  </code></pre>
  <p>If you <code>.view()</code> the <code>ch_reads</code> you get:</p>
  <pre><code>[[id:sample1, single_end:false], [/Users/atpoint/sample1_R1.fq.gz, /Users/atpoint/sample1_R2.fq.gz]]
  [[id:sample2, single_end:true], [/Users/atpoint/sample2_R1.fq.gz]]
  </code></pre>
  <p>A process that can use that could be:</p>
  <pre><code>
  process A {
  
      tag &quot;$meta.id&quot;
  
      input:
      tuple val(meta), path(reads)
  
      script:
      
      // The meta map holds the single/paired information that can now easily be parsed in the module in a standardized way
      if(meta.single_end){
  
          &quot;&quot;&quot;
          do_single_end_things with ${reads}
          &quot;&quot;&quot;
  
      } else {
  
          &quot;&quot;&quot;
          do_paired_end_things <span class="math-container">${reads}[0] $</span>{reads}[1] 
          &quot;&quot;&quot;
          
      }
  
  }
  
  A(ch_reads)
  
  </code></pre>
  <p>The meta map idea (cudos nf-core) is simple, yet versatile and powerful as it allows standardized parsing of such metadata-like information (single_end, libtype, id/sample_name, any other value you can think of) and most importantly, it allows to process single-end paired end data at the same time. All the decision making is based on the meta map and therefore automated if the modules are coded appropriately as above.</p>
  <p>Hope that helps.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-12-22T22:07:28.353Z
Answers.Text: Welcome to the site @ATpoint
Answers.UserDisplayName: M__
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2022-12-22T20:23:26.103Z
Answers.LastActivityDate: 2022-12-22T20:58:29.777Z
Answers.LastEditDate: 2022-12-22T20:58:29.777Z
Answers.UserDisplayName: ATpoint
Body: <p>Suppose you have a pipeline that takes reads as input from the user and trims them.</p>
  <pre><code>// Declare syntax version
  nextflow.enable.dsl=2
  
  /* 
   * pipeline input parameters 
   */
  
  
  params.reads = &quot;$projectDir/data/*_{1,2}.fastq&quot;
  
  
  /*
   * define the `TRIM` process that creates trimmed.reads.fastq files
   * given the reads.fastq file. 
   */
   
  process TRIM {
  
      tag &quot;$pair_id&quot;
  
      input:
      tuple val(pair_id), path(reads)
  
      output:
      path(pair_id)
  
      script:
      &quot;&quot;&quot;
      atria -r <span class="math-container">${reads[0]} -R $</span>{reads[1]} -t 1 -l 12 -q 30 -o $pair_id
      &quot;&quot;&quot;
  }
  
  workflow {
  
      read_pairs_ch = Channel.fromFilePairs( params.reads, checkIfExists:true )
  
      trim_ch=TRIM(read_pairs_ch)
  
  }
  </code></pre>
  <p>This particular one takes paired end reads as input. What if the user wanted to trim both single end and paired end reads, how to account for single end reads as the input?</p>
  <p>Best wishes.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-23T08:27:28.333Z
Comments.Text: Oh yes, I do upvote every response. and after implementing I accept one of the solutions.
Comments.UserDisplayName: pubsurfted
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-23T13:38:13.587Z
Comments.Text: Thanks @pubserfted and Merry Christmas!
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-23T14:02:28.067Z
Comments.Text: @M__ Merry Christmas! Hope you have a good one. ^-^
Comments.UserDisplayName: pubsurfted
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-12-23T14:44:40.843Z
Comments.Text: Thank you @pubsurfted! I'm worked to the bone and will definitely enjoy the vacation.
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-04-02T01:00:22.533Z
Comments.Text: Having to generate a sample sheet is just wasting time when you can detect it from the directory contents.
Comments.UserDisplayName: raygozag
Tags: <nextflow>
Title: How does one account for both single end and paired end reads as input in a Nextflow pipeline?
ThreadText: # How does one account for both single end and paired end reads as input in a Nextflow pipeline?
  
  (Asked by: username_0 on 2022-12-22)
  
  Suppose you have a pipeline that takes reads as input from the user and trims them.
  
  ```
  // Declare syntax version
  nextflow.enable.dsl=2
  
  /* 
   * pipeline input parameters 
   */
  
  params.reads = "$projectDir/data/*_{1,2}.fastq"
  
  /*
   * define the `TRIM` process that creates trimmed.reads.fastq files
   * given the reads.fastq file. 
   */
   
  process TRIM {
  
      tag "$pair_id"
  
      input:
      tuple val(pair_id), path(reads)
  
      output:
      path(pair_id)
  
      script:
      """
      atria -r ${reads[0]} -R ${reads[1]} -t 1 -l 12 -q 30 -o $pair_id
      """
  }
  
  workflow {
  
      read_pairs_ch = Channel.fromFilePairs( params.reads, checkIfExists:true )
  
      trim_ch=TRIM(read_pairs_ch)
  
  }
  
  ```
  
  This particular one takes paired end reads as input. What if the user wanted to trim both single end and paired end reads, how to account for single end reads as the input?
  
  Best wishes.
  
  **Tags:** nextflow
  
  > **Comments:**
  > **username_0**: Oh yes, I do upvote every response. and after implementing I accept one of the solutions.  
  > **username_1**: Thanks @pubserfted and Merry Christmas!  
  > **username_0**: @username_1 Merry Christmas! Hope you have a good one. ^-^  
  > **username_1**: Thank you @username_0! I'm worked to the bone and will definitely enjoy the vacation.  
  > **username_2**: Having to generate a sample sheet is just wasting time when you can detect it from the directory contents.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2022-12-22. Score: 2 | Accepted answer
  
  There are many ways to accomplish this. Assuming you don't need to process single-end and paired-end reads simultaneously (i.e. within the same run), one way using the [`fromFilePairs`](https://www.nextflow.io/docs/latest/channel.html#fromfilepairs) factory method is to just use an additional flag to define the number of files each emitted item is expected to hold. And then adjust your process definition accordingly:
  
  ```
  params.reads = "${projectDir}/data/*_{1,2}.fastq.gz"
  params.singleEnd = false
  
  process TRIM {
  
      tag "${pair_id}"
  
      cpus 1
  
      input:
      tuple val(pair_id), path(reads)
  
      output:
      tuple val(pair_id), path("${pair_id}/*.atria.fastq{,.gz}")
  
      script:
      def single = reads instanceof Path
  
      def read1 = !single ? /-r "${reads[0]}"/ : /-r "${reads}"/
      def read2 = !single ? /-R "${reads[1]}"/ : ''
  
      """
      atria \\
          -t ${task.cpus} \\
          ${read1} \\
          ${read2} \\
          -l 12 \\
          -q 30 \\
          -o "${pair_id}"
      """
  }
  
  ```
  
  ```
  workflow {
  
      Channel
          .fromFilePairs( params.reads, size: params.singleEnd ? 1 : 2 )
          .ifEmpty { error "Could not find any reads matching pattern: ${params.reads}" }
          .set { reads }
  
      TRIM( reads ).view()
  }
  
  ```
  
  Although we've used an additional flag, it does let the pipeline fail immediately if it can't find the files it expects. I think this approach is more explicit and provides a better user experience:
  
  ```
  $ nextflow run main.nf --reads './data/*.fastq'
  N E X T F L O W  ~  version 22.10.0
  Launching `main.nf` [nasty_allen] DSL2 - revision: 2cbc311974
  Could not find any reads matching pattern: ./data/*.fastq
  
   -- Check script 'main.nf' at line: 38 or see '.nextflow.log' file for more details
  
  ```
  
  Doh! I forgot that these are single ended reads:
  
  ```
  $ nextflow run main.nf --reads './data/*.fastq' --singleEnd
  N E X T F L O W  ~  version 22.10.0
  Launching `main.nf` [clever_gutenberg] DSL2 - revision: 2cbc311974
  executor >  local (3)
  [8e/f90c90] process > TRIM (X) [100%] 3 of 3 ✔
  [Y, /path/to/work/e6/48df1485bb7de8355ed8ce0f1b53da/Y/Y.atria.fastq]
  [Z, /path/to/work/eb/aca3389344ac03ff283ded0c46a7a6/Z/Z.atria.fastq]
  [X, /path/to/work/8e/f90c90210103c03a3fbde697e01227/X/X.atria.fastq]
  
  ```
  
  
  ---
  
  ### Answer by username_4 on 2022-12-22. Score: 2
  
  My personal strategy is to always read data from a samplesheet which then auto-detects whether a sample is paired-end or single-end and stores this information in a so-called meta map (inspired by nf-core) which then passes this information to the modules.
  
  Example:
  
  Say you have a samplesheet that is a three-column csv file with a header:
  
  ```
  $ cat samplesheet.csv 
  sample,r1,r2
  sample1,/Users/username_4/sample1_R1.fq.gz,/Users/username_4/sample1_R2.fq.gz
  sample2,/Users/username_4/sample2_R1.fq.gz,
  
  ```
  
  Read this into Nextflow and detect whether r2 has an entry. If so it is paired-end, else it is single-end:
  
  ```
  
  # main.nf
  
  nextflow.enable.dsl = 2
  
  // Channel for the samplesheet
  ch_samplesheet = Channel.fromPath("/Users/username_4/samplesheet.csv")
  
  // Parse it line by line
  ch_reads = ch_samplesheet.splitCsv(header:true).map {
  
      // This is the read1 and read2 entry
      r1 = it['r1']
      r2 = it['r2']
  
      // Detect wiether single-end or paired-end
      is_singleEnd = r2.toString()=='' ? true : false
      
      // The "meta" map, which is a Nextflow/Groovy map with id (the sample name) and a single_end logical entry
      meta = [id: it['sample'], single_end: is_singleEnd]
      
      // We return a nested map, the first entry is the meta map, the second one is the read(s)
      r2.toString()=='' ? [meta, [r1]] : [meta, [r1, r2]]
  
  }
  
  ```
  
  If you `.view()` the `ch_reads` you get:
  
  ```
  [[id:sample1, single_end:false], [/Users/username_4/sample1_R1.fq.gz, /Users/username_4/sample1_R2.fq.gz]]
  [[id:sample2, single_end:true], [/Users/username_4/sample2_R1.fq.gz]]
  
  ```
  
  A process that can use that could be:
  
  ```
  
  process A {
  
      tag "$meta.id"
  
      input:
      tuple val(meta), path(reads)
  
      script:
      
      // The meta map holds the single/paired information that can now easily be parsed in the module in a standardized way
      if(meta.single_end){
  
          """
          do_single_end_things with ${reads}
          """
  
      } else {
  
          """
          do_paired_end_things ${reads}[0] ${reads}[1] 
          """
          
      }
  
  }
  
  A(ch_reads)
  
  ```
  
  The meta map idea (cudos nf-core) is simple, yet versatile and powerful as it allows standardized parsing of such metadata-like information (single\_end, libtype, id/sample\_name, any other value you can think of) and most importantly, it allows to process single-end paired end data at the same time. All the decision making is based on the meta map and therefore automated if the modules are coded appropriately as above.
  
  Hope that helps.
  
  > **Comments:**
  > **username_1**: Welcome to the site @username_4  
  
  ---
  
  