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+# DeepClone pipelines
+
+## Introduction
+
+This page is to summarize the usage of the pipelines and tools used within the context of DeepClone.
+The main steps are: duplex library preparation protocol, deepUMIcaller, the generation of duplex metrics and deepCSA.
+
+The documentation and basic information regarding DeepClone can be found in the protocols paper that can be found here:
+[protocols.io link](https://www.protocols.io/view/deepclone-an-end-to-end-protocol-to-study-somatic-dm6gp1jodgzp/v2)
+
+You will find the basic list of steps in the website and also the main version of the manuscript and then you can check
+for a more detailed explanation of all the steps in the supplementary document also available in protocols.io.
+
+There are some internal definitions on how we use the pipelines but the access to this information is restricted and
+should be requested internally to the PROMINENT team.
+
+## Duplex protocol
+
+The steps are described in the protocol, and there is an alternative and more useful version of it in the supplementary material.
+We recommend users to use the supplementary material one.
+
+## deepUMIcaller
+
+We use the code available in [deepUMIcaller](https://github.com/bbglab/deepUMIcaller.git), we generally use the dev branch
+since this contains the most updated version of the code and is generally stable.
+
+We run it via Seqera platform so that we have full record of the runs and coordination of the different projects.
+
+We always put the work directory in /scratch and the outputs can either go to the s3 or to nobackup or nobackup2.
+
+If you have to access the s3 either for saving concats or for storing the output of deepUMIcaller there,
+check the [S3 entry](https://bbglab.github.io/bbgwiki/Cluster_basics/s3/#terminal) in this wiki.
+
+## Metrics
+
+These are a set of metrics that help us understand two key aspects: whether our duplex libraries have properly worked and importantly to estimate how much sequencing output should be requested to avoid undersequencing but most importantly oversequencing.  
+
+*When should I run metrics*
+
+Everytime you do a new deepUMIcaller run and before running deepCSA. 
+
+*Why?* 
+
+1. To validate you have included all GBs of data available for that library (all lanes and reseqs)
+2. To check whether you library has been sequenced to optimal or additional reseq needs to be requested 
+3. To continue the effort of compiling these metrics to keep improving our understanding of the duplex protocol
+
+*How*
+
+You can find the instructions on how to run them and additional documentation on metrics in our internal duplex documentation.
+
+## deepCSA
+
+We use the code available in [deepCSA](https://github.com/bbglab/deepCSA.git), we generally use the dev branch
+since this contains the most updated version of the code and is generally stable.
+
+We run it via Seqera platform so that we have full record of the runs and coordination of the different projects.
+
+Add the irbcluster profile when running the pipeline so that the default structural parameters are automatically set.
+
+We always put the work directory in /scratch and the outputs usually in nobackup or nobackup2.
+
+## References
+
+Duplex library prep. protocol:
+
+- Morena Pinheiro
+- Erika López-Arribillaga
+- Nuría Samper
+
+Computational pipelines:
+
+- Ferriol Calvet (main developer)
+- Elisabet Figuerola (owns extensive internal documentation)
+- Rocío Chamorro (in particular for metrics)
+- Miguel Grau (developer)