<p>I believe adding a comma after <code>val(sample_name)</code> on line <code>tuple val(sample_name) path(reads)</code> will solve the issue.</p>
<p>EDIT: Also documented here: <a href="https://github.com/nextflow-io/nextflow/discussions/2714" rel="noreferrer">https://github.com/nextflow-io/nextflow/discussions/2714</a></p>

CC BY-SA 4.0
2024-04-23T15:41:17.373Z
Good eye! I had the same and I was sure something was odd but couldn't "see" the missing comma. The resulting error message is really misleading in this case...
dojuba
CC BY-SA 4.0
2023-06-15T15:47:31.360Z
2023-06-15T17:09:24.247Z
2023-06-15T17:09:24.247Z
haci
<p>I am trying to write a nextflow script below:</p>
<pre><code>/*
 * pipeline input parameters
 */
params.reads = &quot;/path/to/fq/files/&quot;
params.guide_library = &quot;/path/to/guidelibrary/&quot;
params.outdir = &quot;results&quot;

log.info &quot;&quot;&quot;\
    DUAL GUIDE CRISPR QC - N F   P I P E L I N E
    ===================================
    guide library: <span class="math-container">${params.guide_library}
reads        : $</span>{params.reads}
    outdir       : ${params.outdir}
    &quot;&quot;&quot;
    .stripIndent(true)

/*
 * define the `index` process that creates a binary index
 * given the transcriptome file
 */


process READCOUNT {
    input:
    path guide_library
    tuple val(sample_name) path(reads)

    output:
    path &quot;$sample_name&quot;

    script:
    &quot;&quot;&quot;
    exactcounts.py -inputlibrary <span class="math-container">$guide_library -read1 $</span>{reads[0]} -read2 <span class="math-container">${reads[1]} -prefix $</span>sample_name
    &quot;&quot;&quot;
}

workflow {
    Channel
        .fromFilePairs(params.reads, checkIfExists: true)
        .set { read_pairs_ch }
   count_ch = READCOUNT(params.guide_library,read_pairs_ch)
    
}
</code></pre>
<p>But am getting the following error:</p>
<pre><code>Process 'READCOUNT' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context
</code></pre>

<nextflow>
Nextflow - Process has already been used
# Nextflow - Process has already been used

(Asked by: username_0 on 2023-06-15)

I am trying to write a nextflow script below:
/*
 * pipeline input parameters
 */
params.reads = "/path/to/fq/files/"
params.guide_library = "/path/to/guidelibrary/"
params.outdir = "results"

log.info """\
    DUAL GUIDE CRISPR QC - N F   P I P E L I N E
    ===================================
    guide library: ${params.guide_library}
reads        : ${params.reads}
    outdir       : ${params.outdir}
    """
    .stripIndent(true)

/*
 * define the `index` process that creates a binary index
 * given the transcriptome file
 */


process READCOUNT {
    input:
    path guide_library
    tuple val(sample_name) path(reads)

    output:
    path "$sample_name"

    script:
    """
    exactcounts.py -inputlibrary $guide_library -read1 ${reads[0]} -read2 ${reads[1]} -prefix $sample_name
    """
}

workflow {
    Channel
        .fromFilePairs(params.reads, checkIfExists: true)
        .set { read_pairs_ch }
   count_ch = READCOUNT(params.guide_library,read_pairs_ch)
    
}

But am getting the following error:
Process 'READCOUNT' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context

**Tags:** nextflow

---

## 1 answers

### Answer by username_1 on 2023-06-15. Score: 6

I believe adding a comma after `val(sample_name)` on line `tuple val(sample_name) path(reads)` will solve the issue.

EDIT: Also documented here: <https://github.com/nextflow-io/nextflow/discussions/2714>

> **Comments:**
> **username_2**: Good eye! I had the same and I was sure something was odd but couldn't "see" the missing comma. The resulting error message is really misleading in this case...  

---

