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nf-core / demultiplex

Demultiplexing pipeline for sequencing data
https://nf-co.re/demultiplex
MIT License
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Ambiguous sampleSheet.csv structure #116

Closed Gian77 closed 2 months ago

Gian77 commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

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 commented 2 months ago

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