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NationalGenomicsInfrastructure / piper

A genomics pipeline build on top of the GATK Queue framework
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report.tsv is not overwritten when sthlm2UUSNP is run #14

Closed mariogiov closed 10 years ago

mariogiov commented 10 years ago

It appends rather than replacing, which causes Piper to fail:

#SampleName     Lane    ReadLibrary     FlowcellId
P1142_101       1       P1142_101       BC423WACXX
P1142_101       2       P1142_101       BC423WACXX
P1142_101       3       P1142_101       BC423WACXX
P1142_101       4       P1142_101       BC423WACXX
P1142_101       1       P1142_101       BC423WACXX
P1142_101       2       P1142_101       BC423WACXX
P1142_101       3       P1142_101       BC423WACXX
P1142_101       4       P1142_101       BC423WACXX
#SampleName     Lane    ReadLibrary     FlowcellId
P1142_101       1       P1142_101       BC423WACXX
P1142_101       2       P1142_101       BC423WACXX
P1142_101       3       P1142_101       BC423WACXX
P1142_101       4       P1142_101       BC423WACXX
#SampleName     Lane    ReadLibrary     FlowcellId
P1142_101       1       P1142_101       BC423WACXX
P1142_101       2       P1142_101       BC423WACXX
P1142_101       3       P1142_101       BC423WACXX
P1142_101       4       P1142_101       BC423WACXX
#SampleName     Lane    ReadLibrary     FlowcellId
P1142_101       1       P1142_101       BC423WACXX
P1142_101       2       P1142_101       BC423WACXX
P1142_101       3       P1142_101       BC423WACXX
P1142_101       4       P1142_101       BC423WACXX
johandahlberg commented 10 years ago

I think that this is fixed now. Checkout fb1214511b7851647b7505454e00b2b41ddfcd19 and let me know if I actually got it correct this time.

vezzi commented 10 years ago

Works!!!!