Missing required field on nf-core/sopa

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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

# 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

/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:

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.

2

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.