Pipeline stopped in first step (Bcl2FastQ).

Cause: The samplesheet is corrupt.


  • check if there are no Windows signs in the samplesheet (^M) → mac2unix
  • No empty lines at the bottom (NB: empty means only comma’s)
  • Are there required fields written with ‘none’ instead of ‘None’

All the reads are discarded.

Possible cause: There is an unknown barcodeType, the step will crash.

Solution: Fill in a barcodeType in the samplesheet that is valid (and create an issue in molgenis-pipelines on GitHub that a new barcode should be added to the known barcodeTypes.

Pipeline is not producing correct data.

Possible cause: Are there dual barcodes?

In case of dual barcodes, the second barcode should be reversed complement.


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