--protocol is not being properly detected when running with "--aligner kallisto" and "-with-report"

[graemefox]

Description of the bug

Hi team,
I'm running scrnaseq using "--aligner kallisto" and "--protocol 10XV3" alongside "-with-report" and am hitting an issue with protocol apparently not being picked up correctly somewhere.

I can see that my settings are being picked up by Nextflow:

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/scrnaseq 4.1.0
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Input/output options
  input               : /mypath/samplesheet.csv
  outdir              : /mypath/kallisto_output/

Mandatory arguments
  aligner             : kallisto
  protocol            : 10XV3

The pipeline does complete the analysis successfully, but creation of the report is failing:

[a8/f60e54] NFC…_CHECK:FASTQC (pbmc_1k_v3) | 1 of 1 ✔
[43/82bca0] NFC…TF_GENE_FILTER (genome.fa) | 1 of 1 ✔
[dc/62446e] NFC…TOBUSTOOLS_REF (genome.fa) | 1 of 1 ✔
[9f/6602b0] NFC…USTOOLS_COUNT (pbmc_1k_v3) | 1 of 1 ✔
[6c/e91361] NFC…Q:MTX_TO_H5AD (pbmc_1k_v3) | 2 of 2 ✔
[c9/6f0b97] NFC…OVEBACKGROUND (pbmc_1k_v3) | 1 of 1 ✔
[ab/cf5a6a] NFC…DATA_BARCODES (pbmc_1k_v3) | 1 of 1 ✔
[e8/dcdf84] NFC…ION:CONCAT_H5AD (combined) | 3 of 3 ✔
[4a/96d8cd] NFC…NNDATAR_CONVERT (combined) | 6 of 6 ✔
[90/f989cf] NFC…_SCRNASEQ:SCRNASEQ:MULTIQC | 1 of 1 ✔
-[nf-core/scrnaseq] Pipeline completed successfully-
Completed at: 19-Jan-2026 15:46:07
Duration    : 1h 2m 19s
CPU hours   : 7.0
Succeeded   : 18

WARN: Failed to render execution report -- see the log file for details

In the report, I see:

"Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: null.

The full error message was:

Only cellranger supports protocol = 'auto'. Please specify the protocol manually!"

and the command printed in the report is (note that protocol is missing):

nextflow run nf-core/scrnaseq 
-profile singularity 
-with-report /mypath/kallisto_nextflow_report.html 
--input /mypath/samplesheet.csv 
--fasta /mypath/genome.fa 
--gtf /mypath/genes.gtf 
--aligner kallisto 
--outdir /mypath/kallisto_output/

Thanks for all the hard work on these pipelines. If I can provide any more useful info, just let me know.

Graeme

Command used and terminal output

nextflow run nf-core/scrnaseq \
    -profile singularity \
    -with-report /mypath/kallisto_nextflow_report.html \
    --input /mypath/samplesheet.csv \
    --fasta /mypath/genome.fa \
    --gtf /mypath/genes.gtf \
    --aligner kallisto \
    --protocol 10XV3 \
    --outdir /mypath/kallisto_output/

Relevant files

No response

System information

N E X T F L O W ~ version 25.10.2
Hardware = HPC
scrnaseq version = nf-core/scrnaseq 4.1.0
Executor = slurm
Container engine = singularity
OS = Rocky Linux 9.6