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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.
@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.
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
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