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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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allow for extra columns in the sample sheet #323

Closed nick-youngblut closed 1 month ago

nick-youngblut commented 1 month ago

Description of feature

check_samplesheet.py currently requires the input sample sheet to only include specific columns:

        MIN_HEADER = ["sample", "fastq_1", "fastq_2"]
        OPT_HEADER = ["expected_cells", "seq_center", "fastq_barcode", "sample_type"]

There's no need to prevent extra columns, given that they can simply be ignored.

Allowing for extra columns enables the user to include extra metadata in the sample sheet, if they choose.

In my specific case, I could not use: ngs_run,sample,fastq_1,fastq_2, which generated the error:

ERROR: Please check samplesheet header -> ngs_run,sample,fastq_1,fastq_2 != sample,fastq_1,fastq_2

...since ngs_run is not an allowed header.

grst commented 1 month ago

This should already be fixed in the development version and in the upcoming 2.6.0 release.