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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Get rid of checkpoints #20

Open johanneskoester opened 4 years ago

johanneskoester commented 4 years ago

Checkpoints are not needed here anymore, because the report flag now can take a directory and add all contained files into the report, see here.

Hence, we need to replace the boostrap jobs with a single job that iterates over all significant genes and writes the boostrap plots into a directory. That can then be annotated for the report as follows:

report("results/plots/bootstrap", patterns=["{transcript}.bootstrap.pdf"], category=..., caption=...)