Ambiguous sampleSheet.csv structure

[Gian77]

Description of the bug

Hello,

I am trying to run this pipeline to demultiplex an illimina miseq dataset of ITS amplicons. I am kind of confused what should be in the samplesheet. In the .nextflow/assets/nf-core/demultiplex/docs/example_input.csv is reported as

flowcell,samplesheet,lane,run_dir
DDMMYY_SERIAL_NUMBER_FC,/path/to/SampleSheet.csv,1,/path/to/sequencer/output
DDMMYY_SERIAL_NUMBER_FC,/path/to/SampleSheet.csv,2,/path/to/sequencer/output
DDMMYY_SERIAL_NUMBER_FC2,/path/to/SampleSheet2.csv,1,/path/to/sequencer/output2

while in the main page of the nf-core is

id,samplesheet,lane,flowcell
DDMMYY_SERIAL_NUMBER_FC,/path/to/SampleSheet.csv,1,/path/to/sequencer/output
DDMMYY_SERIAL_NUMBER_FC,/path/to/SampleSheet.csv,2,/path/to/sequencer/output
DDMMYY_SERIAL_NUMBER_FC2,/path/to/SampleSheet2.csv,1,/path/to/sequencer/output2
DDMMYY_SERIAL_NUMBER_FC3,/path/to/SampleSheet3.csv,3,/path/to/sequencer/output3

and the description is even more confusing

Column	Description
flowcell	flowcell id
samplesheet	Full path to the SampleSheet.csv file containing the sample information and indexes
lane	Optional lane number. When a lane number is provided, only the given lane will be demultiplexed
run_dir	Full path to the Illumina sequencer output directory or a tar.gz file containing the contents of said directory

I tried both version but I got this an error back. What is the right way to specify this paramter? Thanks a lot, Gian

Command used and terminal output

nextflow run \
	nf-core/demultiplex \
	--input samplesheet.csv \
	--outdir demux_results \
	-profile singularity

Relevant files

No response

System information

22.10.6

[AdrijaK]

Hi Gian, did you first try to run the pipeline in test mode to figure out if this is a pipeline issue or a samplesheet issue?

nextflow run nf-core/demultiplex -profile test --outdir demux_results 

meanwhile, to my knowledge the samplesheet.csv header should work for -r 1.3.1:

id,samplesheet,lane,flowcell

[edmundmiller]

Thanks! We're discussing this on #98

I tried both version but I got this an error back.

What's the error? I'm not seeing any section of your issue that lists an error.

pipeline issue or a samplesheet issue

Or a platform issue.

[atrigila]

This has been addressed in https://github.com/nf-core/demultiplex/pull/201