if run_differential set to False, CONTRAST_KEY variable is not created. This causes the following error:
NameError in line 133 of /SAN/vyplab/sbs_projects/pipelines/doubles/triples/PAPA/rules/differential_apa.smk:
name 'CONTRAST_NAME' is not defined
File "/SAN/vyplab/sbs_projects/pipelines/doubles/triples/PAPA/Snakefile", line 71, in <module>
File "/SAN/vyplab/sbs_projects/pipelines/doubles/triples/PAPA/rules/differential_apa.smk", line 133, in <module>
Solution is to no longer wrap the construction of the variable in the if loop, or alternatively the contrast name can be set to a dummy value (e.g. NULL). I think dummy value would be preferable as can allow users to not provide two conditions in sample table if wish to not run differential usage analysis.
if run_differential set to False, CONTRAST_KEY variable is not created. This causes the following error:
Solution is to no longer wrap the construction of the variable in the if loop, or alternatively the contrast name can be set to a dummy value (e.g. NULL). I think dummy value would be preferable as can allow users to not provide two conditions in sample table if wish to not run differential usage analysis.