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nf-core / scrnaseq

A single-cell RNAseq pipeline for 10X genomics data
https://nf-co.re/scrnaseq
MIT License
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Issues with samplesheet.csv as well as additional columns in the samplesheet #303

Closed SethMagnusJarvis closed 3 months ago

SethMagnusJarvis commented 4 months ago

Description of the bug

I tried running the pipeline using the samplesheet and it gave me an error complaining about the number of column names. This disappeared when I remove the sample columns.

According to this post on slack, this apparently shouldn't be an issue "https://nfcore.slack.com/archives/CHN5BV5DW/p1679325616556869"

Either way, the samplesheet should probably be edited so it works.

Command used and terminal output

nextflow run nf-core/scrnaseq --input ./samplesheet.csv --outdir /rds/general/user/user/home/test_results/scrna --genome GRCh38 -profile imperial, standard --aligner cellranger

Relevant files

No response

System information

No response

muharif commented 4 months ago

Hi Seth, I am experiencing the same problem. How did you solve it? I tried to remove the sample column, but it is still showing the same error.

Thanks!

SethMagnusJarvis commented 4 months ago

@muharif The sample sheet had 5 columns, I had to remove everything that wasn't sample,fastq_1,fastq_2. I haven't got the pipeline working, but the error changed so I think it resolved it.

grst commented 3 months ago

Hi,

this issue should be fixed in the development version. You can give it a try with nextflow run ... -r dev. If it doesn't work, please let me know!