Lack of samplesheet template

[SinaMhdn95]

Description of the bug

Hi,
Unfortunately, there is no specific guidance for creating samplesheets for the methylarray module on nf-core or GitHub. The available samplesheet guidance is for FASTQ files, which are not the correct input for this module. I’ve tried several samplesheets to run the pipeline, but none of them have worked.

Command used and terminal output

input in the shell:
#!/bin/bash
#SBATCH --job-name=methylarray
#SBATCH --output=nextflow_methylarray.log
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=16
#SBATCH --mem=64G
#SBATCH --time=24:00:00
nextflow run nf-core/methylarray \
  --input samplesheet2.csv \
  --idat_dir /lustre/home/mahdianis/aging_HF/idat_files \
  --outdir ./methylarray_output \
  -profile singularity \
  -r dev

output: 
1. ERROR ~ Error executing process > 'NFCORE_METHYLARRAY:METHYLARRAY:PREPROCESS (/lustre/home/mahdianis/aging_HF/SampleSheet2.csv)'

Caused by:
  Process NFCORE_METHYLARRAY:METHYLARRAY:PREPROCESS (/lustre/home/mahdianis/aging_HF/SampleSheet2.csv) terminated with an error exit status (1)

2. Command error:
  The following object is masked from ‘package:MatrixGenerics’:
      rowMedians
  
  The following objects are masked from ‘package:matrixStats’:
      anyMissing, rowMedians

3.Error in list.files(path = base, pattern = "_Grn.idat$", recursive = recursive,  : 
    invalid 'path' argument
  Calls: read.metharray.exp -> list.files
  Execution halted

Relevant files

samplesheet2.csv

System information

Nextflow version: 25.04.2.5947
Hardware: HPC (Athena cluster)
Executor: slurm
Container engine: Singularity
OS: CentOS Linux
Version of nf-core/methylarray: dev

[ajandria]

Hi, it should be improved with #33