# Fastq columns in nf-core pipeline even though they are not part of the samplesheet

**URL:** <https://community.seqera.io/t/fastq-columns-in-nf-core-pipeline-even-though-they-are-not-part-of-the-samplesheet/1715>\
**Category:** Ask for help\
**Created:** [February 6, 2025, 4:58pm UTC](https://community.seqera.io/t/fastq-columns-in-nf-core-pipeline-even-though-they-are-not-part-of-the-samplesheet/1715 "2025-02-06T16:58:29Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![ramirobarrantes](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ramirobarrantes/32/717_2.png) [@ramirobarrantes](https://community.seqera.io/u/ramirobarrantes)\
**Post date:** [February 6, 2025, 4:58pm UTC](https://community.seqera.io/t/fastq-columns-in-nf-core-pipeline-even-though-they-are-not-part-of-the-samplesheet/1715/1 "2025-02-06T16:58:29Z")

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I created a pipeline using the nf-core framework. I got a strange error that happened at the sample sheet level, my samplesheet has five columns:

sample,bam,bai,vcf,tbi  
(notice no fastq anywhere)

and as I was digging in I saw the following on subworkflows/local/utils\_nfcore\_my\_pipeline:

```
//
// Create channel from input file provided through params.input
//

```

```auto
    Channel
        .fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
        .map {
            meta, fastq_1, fastq_2 ->
                if (!fastq_2) {
                    return [meta.id, meta + [ single_end:true], [fastq_1] ]
                } else {
                    return [meta.id, meta + [ single_end:false], [fastq_1, fastq_2] ]
                }
        }
        .groupTuple()
        .map { samplesheet ->
            validateInputSamplesheet(samplesheet)
        }
        .map {
            meta, fastqs ->
                return [meta, fastqs.flatten()]
        }
        .set { ch_samplesheet }

```

Which referes to fastqs ,etc. It seems that I need to edit this file?

---

<div class="post-metadata">

**Author:** ![ramirobarrantes](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ramirobarrantes/32/717_2.png) [@ramirobarrantes](https://community.seqera.io/u/ramirobarrantes)\
**Post date:** [February 6, 2025, 8:17pm UTC](https://community.seqera.io/t/fastq-columns-in-nf-core-pipeline-even-though-they-are-not-part-of-the-samplesheet/1715/2 "2025-02-06T20:17:27Z")

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For anybody seeing this, it was answered on slack by @Alexander_Nater: " Alexander NaterAlexander Nater [Today at 1:01 PM](https://nfcore.slack.com/archives/CE6SDBX2A/p1738864919852489?thread_ts=1738864103.595969&cid=CE6SDBX2A)

Yes, you need to edit the `assets/schema_input.json` and the `subworkflows/local/utils_nfcore_my_pipeline` to match the structure of your samplesheet."

---

<div class="post-metadata">

**Author:** ![ramirobarrantes](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/ramirobarrantes/32/717_2.png) [@ramirobarrantes](https://community.seqera.io/u/ramirobarrantes)\
**Post date:** [February 13, 2025, 8:17pm UTC](https://community.seqera.io/t/fastq-columns-in-nf-core-pipeline-even-though-they-are-not-part-of-the-samplesheet/1715/3 "2025-02-13T20:17:41Z")

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