Answers.Body: <p>If you are certain your input files exist, I think the issue might be that the <a href="https://www.nextflow.io/docs/latest/channel.html#frompath" rel="nofollow noreferrer">fromPath</a> factory method emits file paths, but your <em>ALIGNMENT</em> process is expecting a <a href="https://www.nextflow.io/docs/latest/process.html#input-type-tuple" rel="nofollow noreferrer">tuple</a>. One solution is to use the <a href="https://www.nextflow.io/docs/latest/operator.html#map" rel="nofollow noreferrer">map</a> operator to transform the input channel into a tuple, for example (untested and ignoring the publishDir directive):</p>
  <pre><code>params.reads = '/Volumes/matthews/AHR_ER_project_files/FASTQ/TCDD_AHR_Rep_ChIPSeq_1.fastq.gz'
  params.genome = '/Users/siddhaduio.no/Desktop/All_omics_tools/bowtie2-2.4.4-macos-x86_64/hg38_index/human_hg38_index.*.bt2'
  </code></pre>
  <pre><code>process ALIGNMENT {
  
      tag &quot;ALIGNMENT ${sample_id}&quot;
  
      conda 'bowtie2'
  
      input:
      tuple val(sample_id), path(reads)
      path bowtie_index
  
      output:
      tuple val(sample_id), path(&quot;{sample_id}.aligned.bam&quot;), emit: aligned_bam
  
      script:
      def bt2_idx = bowtie_index[0].simpleName
  
      &quot;&quot;&quot;
      bowtie2 \\
          -p 64 \\
          -q \\
          -x &quot;<span class="math-container">${bt2_idx}" \\
          -U "$</span>{reads.join(',')}&quot; \\
          -S &quot;${sample_id}.aligned.bam&quot;
      &quot;&quot;&quot;
  }
  </code></pre>
  <pre><code>workflow {
  
      fastq_reads = channel.fromPath( params.reads ).map { fastq -&gt;
          tuple( fastq.simpleName, fastq )
      }
  
      bowtie_index_files = files( params.genome )
  
  
      ALIGNMENT( fastq_reads, bowtie_index_files )
  }
  </code></pre>
  <p>Run using:</p>
  <pre><code>nextflow run main.nf -with-conda
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-09-08T23:40:00.157Z
Answers.LastActivityDate: 2024-09-08T23:40:00.157Z
Answers.UserDisplayName: Steve
Body: <p>I am trying to learn nextflow and use the process and workflow below to align some Chip seq reads.</p>
  <p>For the command below, I am getting the error: <code>Path value cannot be null</code></p>
  <p>My genome index files are named <code>human_hg38_index.*.bt2</code> within the folder that I have specified within <code>params.genome</code>.</p>
  <p>I was wondering how do I fix this error?</p>
  <p>Thanks!</p>
  <pre><code>#!/usr/bin/env nextflow
  
  params.reads = '/Volumes/matthews/AHR_ER_project_files/FASTQ/TCDD_AHR_Rep_ChIPSeq_1.fastq.gz'
  params.genome = '/Users/siddhaduio.no/Desktop/All_omics_tools/bowtie2-2.4.4-macos-x86_64/hg38_index/'
  params.outdir = '/Volumes/matthews/AHR_ER_project_files/FASTQ/results'
  
  workflow {
    fastq_reads = channel.fromPath(params.reads)
    index_file= channel.fromPath(params.genome)
  
    ALIGNMENT(index_file,fastq_reads)
  }
  
  process ALIGNMENT {
    tag {&quot;ALIGNMENT {sample_id}&quot;} 
    label 'bowtie2'
      publishDir &quot;${params.outdir}/bowtie2_align&quot;, mode:'copy', pattern: &quot;*.bam&quot;
  
    input:
  
      path genome
      tuple val( sample_id ), path( reads )
  
    output:
  
      path( &quot;{sample_id}.aligned.bam&quot; ), emit: aligned_bam
  
    script:
      &quot;&quot;&quot;
      /Users/siddhaduio.no/Desktop/All_omics_tools/bowtie2-2.4.4-macos-x86_64/bowtie2 -p 64 -q -x {genome} -U {sample_id}.fastq.gz -S {sample_id}.aligned.bam
      &quot;&quot;&quot;
  } 
  </code></pre>
  
Tags: <nextflow>
Title: Path value cannot be null error in nextflow
ThreadText: # Path value cannot be null error in nextflow
  
  (Asked by: username_0 on 2024-09-08)
  
  I am trying to learn nextflow and use the process and workflow below to align some Chip seq reads.
  
  For the command below, I am getting the error: `Path value cannot be null`
  
  My genome index files are named `human_hg38_index.*.bt2` within the folder that I have specified within `params.genome`.
  
  I was wondering how do I fix this error?
  
  Thanks!
  
  ```
  #!/usr/bin/env nextflow
  
  params.reads = '/Volumes/matthews/AHR_ER_project_files/FASTQ/TCDD_AHR_Rep_ChIPSeq_1.fastq.gz'
  params.genome = '/Users/siddhaduio.no/Desktop/All_omics_tools/bowtie2-2.4.4-macos-x86_64/hg38_index/'
  params.outdir = '/Volumes/matthews/AHR_ER_project_files/FASTQ/results'
  
  workflow {
    fastq_reads = channel.fromPath(params.reads)
    index_file= channel.fromPath(params.genome)
  
    ALIGNMENT(index_file,fastq_reads)
  }
  
  process ALIGNMENT {
    tag {"ALIGNMENT {sample_id}"} 
    label 'bowtie2'
      publishDir "${params.outdir}/bowtie2_align", mode:'copy', pattern: "*.bam"
  
    input:
  
      path genome
      tuple val( sample_id ), path( reads )
  
    output:
  
      path( "{sample_id}.aligned.bam" ), emit: aligned_bam
  
    script:
      """
      /Users/siddhaduio.no/Desktop/All_omics_tools/bowtie2-2.4.4-macos-x86_64/bowtie2 -p 64 -q -x {genome} -U {sample_id}.fastq.gz -S {sample_id}.aligned.bam
      """
  } 
  
  ```
  
  **Tags:** nextflow
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2024-09-08. Score: 2
  
  If you are certain your input files exist, I think the issue might be that the [fromPath](https://www.nextflow.io/docs/latest/channel.html#frompath) factory method emits file paths, but your *ALIGNMENT* process is expecting a [tuple](https://www.nextflow.io/docs/latest/process.html#input-type-tuple). One solution is to use the [map](https://www.nextflow.io/docs/latest/operator.html#map) operator to transform the input channel into a tuple, for example (untested and ignoring the publishDir directive):
  
  ```
  params.reads = '/Volumes/matthews/AHR_ER_project_files/FASTQ/TCDD_AHR_Rep_ChIPSeq_1.fastq.gz'
  params.genome = '/Users/siddhaduio.no/Desktop/All_omics_tools/bowtie2-2.4.4-macos-x86_64/hg38_index/human_hg38_index.*.bt2'
  
  ```
  
  ```
  process ALIGNMENT {
  
      tag "ALIGNMENT ${sample_id}"
  
      conda 'bowtie2'
  
      input:
      tuple val(sample_id), path(reads)
      path bowtie_index
  
      output:
      tuple val(sample_id), path("{sample_id}.aligned.bam"), emit: aligned_bam
  
      script:
      def bt2_idx = bowtie_index[0].simpleName
  
      """
      bowtie2 \\
          -p 64 \\
          -q \\
          -x "${bt2_idx}" \\
          -U "${reads.join(',')}" \\
          -S "${sample_id}.aligned.bam"
      """
  }
  
  ```
  
  ```
  workflow {
  
      fastq_reads = channel.fromPath( params.reads ).map { fastq ->
          tuple( fastq.simpleName, fastq )
      }
  
      bowtie_index_files = files( params.genome )
  
      ALIGNMENT( fastq_reads, bowtie_index_files )
  }
  
  ```
  
  Run using:
  
  ```
  nextflow run main.nf -with-conda
  
  ```
  
  
  ---
  
  