Error: “Unrecognized parameter markers” when using params.yml with qptiff input

[PranavMotarwar]

Hi MCMICRO team,

We’re trying to run MCMICRO on NYU Greene HPC with pre-stitched .qptiff files. Based on previous discussion, we’ve configured our params.yml and directory structure as suggested.

However, when executing the pipeline with the following params.yml:

params.yml

workflow:
start-at: segmentation
multi-formats: qptiff
segmentation-channel: 1

The job fails with:

ERROR ~ Unrecognized parameter markers

-- Check script '/home/pm3891/.nextflow/assets/labsyspharm/mcmicro/main.nf' at line: 21 or see '.nextflow.log' file for more details

Directory Structure:

/scratch/pm3891/mcmicro_pipeline/
├── registration/registration_alt/EVA_TMA_Scan1.er.qptiff
├── markers.csv
├── params.yml
└── mcmicro_output.log

markers.csv:

marker_name
AQP1
Axl
b-Catenin1
...

Command used:

nextflow run labsyspharm/mcmicro
--in /scratch/pm3891/mcmicro_pipeline/registration/registration_alt
-profile singularity
-params-file /scratch/pm3891/mcmicro_pipeline/params.yml

Question:
1. Is the error caused by the use of marker-file: instead of markers: or something else?
2. Is multi-formats: qptiff correctly recognized when using the latest main.nf revision?
3. Is this related to expected syntax in the top-level params.yml vs. workflow: block?

[ArtemSokolov]

Hi @PranavMotarwar,

Can you try doing just

nextflow run labsyspharm/mcmicro \
 --in /scratch/pm3891/mcmicro_pipeline \
 -profile singularity

-params-file uses Nextflow's parameter parser, which I think is conflicting with how MCMICRO is trying to read it. To feed an external params file to MCMICRO you would use --params myparams.yml, but in this case it's not needed, because the file lives in the project directory already.