Missing required field on nf-core/sopa

Question

[jomagrax]

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/main/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_pathROI1,/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 [e-mail] 

The problem

ERROR ~ Validation of pipeline parameters failed!Entry 1: Missing required field(s): fastq_1Entry 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.

[Pierre Lindenbaum]

"This is the development version of the pipeline". You should ask the dev on slack "For further information or help, don’t hesitate to get in touch on the Slack #sopa channel (you can join with this invite)."

[jomagrax]

Thank you! But there's something I might be missing because I cant seem to find any invitation to the sopa slack channel

[Maxime Garcia]

To join slack, you can use the link for slack on nf-core. And then join the #sopa channel, either directly on slack or with this link

[ATpoint]

The spambot got triggered here, sorry. Restored your post. I will reach out to the admin to see whether we can train it to not confuse the nf-core links and channel hashes with spam.

[Maxime Garcia]

yeah, no worries, I think OP got there in the end

Answer 1

[Pierre Lindenbaum]

try with :

--validate_params=false

was https://github.com/nf-core/sopa/blob/c991e413df3b52cf459ef06d7daeb1fbc92c9b52/nextflow.config#L51

[jomagrax]

I get rid off some ugly warnings with this, Im afraid the main error still persists