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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
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Changes in `units.tsv` do not promt a rerun of the workflow #10

Open HenningTimm opened 4 years ago

HenningTimm commented 4 years ago

When an entry is added to or removed from units.tsv, this should prompt a rerun of the whole workflow, at least from rules sleuth_init and compose_samplesheet onward. This is currently not the case.

This is might be caused by the compose_sample_sheet rule, which assembles a sample sheet for sleuth from the output of kallisto and the samples file. It is possible that changes to the units file are not properly propagated to this rule. It might be enough, to add units.tsv as an input for this rule.

Another potential point of failure could be the checkpoint sleuth_diffexp.