# Missing required field on nf-core/sopa

**URL:** <https://community.seqera.io/t/missing-required-field-on-nf-core-sopa/2459>\
**Category:** Ask for help\
**Tags:** nextflow, nf-core\
**Created:** [November 19, 2025, 3:53pm UTC](https://community.seqera.io/t/missing-required-field-on-nf-core-sopa/2459 "2025-11-19T15:53:01Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Jose\_Gracia](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/jose_gracia/32/2170_2.png) [@Jose\_Gracia](https://community.seqera.io/u/Jose_Gracia)\
**Post date:** [November 19, 2025, 3:53pm UTC](https://community.seqera.io/t/missing-required-field-on-nf-core-sopa/2459/1 "2025-11-19T15:53:01Z")

</div>

Hi everyone,

I’m trying to run **nf-core/sopa** on my **MACSima** imaging samples.  
I’m working on a **RedHat HPCC environment** , using:

- **Nextflow version:** 25.10.0

- **nf-core/sopa revision:** master (commit 11b4cccb7e)

- **Container engine:** Singularity

* * *

### **My config.yml**

```auto
# For parameters details, see this commented example: https://github.com/gustaveroussy/sopa/blob/df30da607cea4326d7ea907dbec86cb2bca078b3/workflow/config/example_commented.yaml
read:
  technology: macsima

patchify:
  patch_width_pixel: 3000
  patch_overlap_pixel: 40

segmentation:
  cellpose:
    diameter: 35
    channels: ["DAPI"]
    flow_threshold: 2
    cellprob_threshold: -6
    min_area: 400

aggregate:
  aggregate_channels: true
  min_intensity_ratio: 0.1
  expand_radius_ratio: 0.1

explorer:
  ram_threshold_gb: 4
  pixel_size: 0.170

```

**My samplesheet.csv**

`sample,data_path`  
`ROI1,/storage/scratch01/groups/lc/rnafusion_pdx/sopa/sample1/`  
`ROI2,/storage/scratch01/groups/lc/rnafusion_pdx/sopa/sample2/`

The directory contains the MACSima output (multiple TIFFs).

### **Command used**

```auto
/home/jgracia/bin/nextflow run nf-core/sopa -profile singularity --input samplesheet.csv -params-file config.yml --outdir /storage/scratch01/groups/lc/rnafusion_pdx/sopa/ --email josearacena111@gmail.com 

```

### **The problem**

`ERROR ~ Validation of pipeline parameters failed!`  
`Entry 1: Missing required field(s): fastq_1`  
`Entry 2: Missing required field(s): fastq_1`

Even though I explicitly set:

```auto
read:
  technology: macsima

```

This doesn’t make much sense since MACSima doesn’t produce reads of any kind, and since the tecnology used is specified I’m not sure how to solve the error.

---

<div class="post-metadata">

**Author:** ![mahesh.binzerpanchal](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/mahesh.binzerpanchal/32/253_2.png) [@mahesh.binzerpanchal](https://community.seqera.io/u/mahesh.binzerpanchal)\
**Post date:** [November 21, 2025, 9:52am UTC](https://community.seqera.io/t/missing-required-field-on-nf-core-sopa/2459/2 "2025-11-21T09:52:20Z")

</div>

I think you need to use the `dev` branch as the workflow doesn’t have a release version yet.

Modify your nextflow command to use `-r dev` as well.