search

eastgenomics / eggd_dias_batch

1 stars 2 forks source link

automate CNV indications stripping #178

Open kjwinfield opened 8 months ago

kjwinfield commented 8 months ago

Currently samples are booked in Epic with both the SNV and CNV clinical indications. To allow eggd_dias_batch to correctly set off reports, the CNV indications need to be stripped off.

This command is run manually on Epic manifests before running eggd_dias_batch

for test_code in $(dx cat project-Fkb6Gkj433GVVvj73J7x8KbV:file-GXGx8q0433GgKqx52Jqz1p47); 
do sed -i s/${test_code}/""/g <epic-manifest-file> ;
done

It would be good if eggd_dias_batch could do this automatically Note: new test directory might make this no longer needed?

Addy81 commented 8 months ago

In new genepanels includes all those indications this won't be needed in batch.

jethror1 commented 7 months ago

some work started on this here for future me to remember: https://github.com/eastgenomics/eggd_dias_batch/tree/v3.1.0-improve_test_code_handling