Pipeline run

[Mau-sumi-lab]

Description of the bug

I have been trying to run a test data miseq35147139, it's throwing me an error:
ERROR ~ Error executing process > 'NFCORE_DEMULTIPLEX:DEMULTIPLEX:SAMSHEE (run1)'

Caused by:
Process NFCORE_DEMULTIPLEX:DEMULTIPLEX:SAMSHEE (run1) terminated with an error exit status (4)

Command executed:

Run validation command and capture output

python -m samshee run1.lane1_no_adapters.csv > run1.lane1_no_adapters_formatted.csv

cat <<-END_VERSIONS > versions.yml
"NFCORE_DEMULTIPLEX:DEMULTIPLEX:SAMSHEE":
samshee: $( python -m pip show --version samshee | grep "Version" | sed -e "s/Version: //g" )
python: $( python --version | sed -e "s/Python //g" )
END_VERSIONS

Command exit status:
4

Command output:
(empty)

Command error:
failed writing output: validator #0 ({'$ref': 'urn:samshee:illuminav2/v1'}) raised validation errors:

• $.Header: 'FileFormatVersion' is a required property
• $.Header: 'Experiment Name' does not match '^[a-zA-Z0-9_]+$'
• $.Reads: [{'151': 151}] is not of type 'object'

Work dir:
/mnt/sk01sm01/users/mausumi/demultiplex/work/41/0499dc73f9ffb2888c7e6a4a43757a

Container:
/mnt/sk01sm01/users/mausumi/demultiplex/work/singularity/community-cr-prod.seqera.io-docker-registry-v2-blobs-sha256-87-874139c488abfe0d65786bdbafea96a0768554c1a5e8e70a332708954b96dee7-data.img

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details

the pipeline_sheet.csv is:
id,samplesheet,lane,flowcell
run1,mausumi/demultiplex/miseq_35147139_samplesheet.csv,1,mausumi/demultiplex/miseq_35147139

Command used and terminal output

nextflow run nf-core/demultiplex -r 1.6.1 -profile singularity --input pipeline_sheet.csv --outdir results

Relevant files

No response

System information

nextflow version: 25.04.4
executor: local
container engine: singularity
OS: Linux
version of nf-core/demultiplex: 1.6.1

[apeltzer]

This is an issue in your samplesheet, see the error:

failed writing output: validator #0 ({'$ref': 'urn:samshee:illuminav2/v1'}) raised validation errors:

$.Header: 'FileFormatVersion' is a required property
$.Reads: [{'151': 151}] is not of type 'object'

[Mau-sumi-lab]

Hey, The particular samplesheet you are seeing is actually taken from nfcore/testdata. They weren't generated from my end. I did a dry run in order to know how demultiplex Is to be handled. Regards

…

________________________________ From: Alexander Peltzer ***@***.***> Sent: 09 December 2025 18:24 To: nf-core/demultiplex ***@***.***> Cc: Mausumi Behera ***@***.***>; Author ***@***.***> Subject: Re: [nf-core/demultiplex] Pipeline run (Issue #339) [https://avatars.githubusercontent.com/u/2359510?s=20&v=4]apeltzer left a comment (nf-core/demultiplex#339)<#339 (comment)> This is an issue in your samplesheet, see the error: failed writing output: validator #0 ({'$ref': 'urn:samshee:illuminav2/v1'}) raised validation errors: $.Header: 'FileFormatVersion' is a required property $.Reads: [{'151': 151}] is not of type 'object' — Reply to this email directly, view it on GitHub<#339 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BMGEIYN2SHR2NF2ZIGNHHX34A3A6RAVCNFSM6AAAAACCNO76C6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTMMZSGEZDEMRSGQ>. You are receiving this because you authored the thread.Message ID: ***@***.***>

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[grst]

It's probably a v1 samplesheet. Can you try the --v1_schema flag?

[grst]

Hi @Mau-sumi-lab, closing this because there was no further activity. Feel free to reopen if this is still an issue.