Error running nanoseq 3.1.0 with input_path to Nanopore fastq_pass directory

[tamuanand]

Description of the bug

Hi

I am using a git cloned version of nanoseq 3.1.0 and the pipeline does not go beyond the NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK step.

Details below:

I have my samplesheet like this - where the directory <path_to_WT_1_fastqs_from_fastq_pass> and so on contains bunch of fastq.gz files from the fatsq_pass directory after demultiplexing following ONT sequencing run

group,replicate,barcode,input_file,fasta,gtf
sample_WT,1,,<path_to_WT_1_fastqs_from_fastq_pass>,<path_to_fasta>,<path_to_gtf>
sample_WT,2,,<path_to_WT_2_fastqs_from_fastq_pass>,<path_to_fasta>,<path_to_gtf>
sample_KO,1,,<path_to_KO_1_fastqs_from_fastq_pass>,<path_to_fasta>,<path_to_gtf>
sample_KO,2,,<path_to_KO_2_fastqs_from_fastq_pass>,<path_to_fasta>,<path_to_gtf>

When I have the above samplesheet and try to run the nanoseq pipeline, it always errs out at the 1st step - NFCORE_NANOSEQ:NANOSEQ:INPUT_CHECK:SAMPLESHEET_CHECK

Question: What's the correct way to specify this in the samplesheet?

Command used and terminal output

nextflow -log nfcore_nanoseq.log run -bg /path_to_git_cloned_nanoseq/main.nf --input ./samplesheet.csv --protocol cDNA --skip_demultiplexing -profile singularity -ansi-log false 


Command output:
  ERROR: Please check samplesheet -> path does not end with ".fastq.gz", ".fq.gz", or ".bam" and is not an existing directory with correct fast5 and/or fastq inputs.

Command wrapper:
  ERROR: Please check samplesheet -> path does not end with ".fastq.gz", ".fq.gz", or ".bam" and is not an existing directory with correct fast5 and/or fastq inputs.

Relevant files

No response

System information

• Nextflow version - 25.04.3
• Hardware - HPC
• Executor - slurm
• Container engine: apptainer
• OS - RHEL
• Version of nf-core/nanoseq- 3.1.0

[mdhitch]

I have a similar issue using a submission script and sample sheet format that has worked well previously.

[rugilemat]

Have either of you had any luck solving this? I'm been having the same issue.