... | ... | @@ -48,7 +48,10 @@ Test your configuration with a dry run: |
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```sh
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snakemake -nrp --config conf="config.json"
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```
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If everything is fine, the pipeline **SHOULD NOT** run the `split_fastq` rule as it should find the already created `XXX.fastq.gz` in the `CUTADAPT` directory of your previously analyzed data. If this is not the case, have a look at the reasons why snakemake wants to create these files again by looking at the output of the dry run.
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If everything is fine, the pipeline **SHOULD NOT** run the `split_fastq` rule as it should find the already created `XXX.fastq.gz` in the `CUTADAPT` directory of your previously analyzed data. If this is not the case, have a look at the reasons why snakemake wants to create these files again by looking at the output of the dry run. My guess is that you did not specify the parent directory of the NTS-XXX folder with the `-w` argument of the `make_srp_config.py` script.
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You can now launch the pipeline in cluster mode according to the main page of the project:
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https://gitlab.univ-nantes.fr/bird_pipeline_registry/srp-pipeline
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#### Re-analyzing with sample splitting into multiple projects
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... | ... | |