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bihealth / digestiflow-demux

:spaghetti: Digestiflow Demultiplexing Tool
MIT License
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Unindexed runs do not produce Undetermined.fastq.gz, but snakemake expects them #12

Closed messersc closed 5 years ago

messersc commented 5 years ago

Bug

Lanes without index reads to not produce Undetermined reads, as all reads belong to the one sample loaded.

Undetermined_*’: No such file or directory

Fix

In case of now index reads configured (no B in bases mask), do not expect Undetermined* output files.

Should be fixed together with https://github.com/bihealth/digestiflow-demux/issues/10

messersc commented 5 years ago

@holtgrewe

Fixed in the bcl2fastq2 wrapper, which does not try do copy non-existing Undetermined* files anymore.

Fixed in the snakemake workflow for flow cells with no index read.

Not fixed for flow cells with perfect index reads.

holtgrewe commented 5 years ago

Fixed in current master.