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.