RNAflow is a snakemake pipeline dedicated to standard transcriptomic analysis.
RNAflow is a snakemake pipeline dedicated to standard transcriptomic analysis [@Hub of Bioinformatics & Biostatistics](https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/).
Be careful, RNAflow was principally conceived to run on the HPC of Institut Pasteur, and not on other HPC.
Be careful, RNAflow was principally conceived to run on the HPC of Institut Pasteur, and not on other HPC.
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@@ -49,19 +50,25 @@ If you simply want to use this workflow, download and extract the latest release
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@@ -49,19 +50,25 @@ If you simply want to use this workflow, download and extract the latest release
* Step 2: Configure workflow
* Step 2: Configure workflow
Configure the workflow according to your needs via editing the config.yaml and multiqc_config.yaml files in the config/ directory.
Configure the workflow according to your needs via editing the [config.yaml](https://gitlab.pasteur.fr/hub/rnaflow/-/blob/master/config/config.yaml) and [multiqc_config.yaml](https://gitlab.pasteur.fr/hub/rnaflow/-/blob/master/config/multiqc_config.yaml) files in the `config/` directory.
* Step 3: Load your conda environment
See [runme.sh](https://gitlab.pasteur.fr/hub/rnaflow/-/blob/master/runme.sh) to create the complete conda env.
`conda activate snakemake`
* Step 3: Execute workflow
* Step 4: Execute workflow
Test your configuration by performing a dry-run via
Test your configuration by performing a dry-run via