add DeepClone page to pipelines

Author: FerriolCalvet

docs/pipelines/DeepClone.md

@@ -0,0 +1,138 @@
+# DeepClone pipelines
+
+## deepUMIcaller
+
+## Metrics
+
+## deepCSA
+
+<!-- 
+TODO: Brief introduction on what is intogen - its website and its purpose, use webs and repo as reference.
+-->
+[![GitHub](https://img.shields.io/badge/github-%23121011.svg?style=for-the-badge&logo=github&logoColor=white)](https://github.com/bbglab/intogen-plus-dsl2/)<!-- markdownlint-disable MD013 -->
+
+It's a framework for automatic and comprehensive knowledge extraction based on mutational data from
+sequenced tumor samples from patients.
+
+## Run IntOGen DSL2
+
+Great effort was put to migrate IntOGen from nextflow DSL1 to nextflow DSL2. This effort allowed to be able to run the
+pipeline within our seqera platform dashboard.
+
+From the bbglabirb/ALP_pipelines workspace [launchpad](https://cloud.seqera.io/orgs/bbglabirb/workspaces/ALP_pipelines/launchpad),
+you can access the pipelines available in our workspace.
+
+!!! question "I can't see the workspace, what should I do?"
+    Please refer to Miguel or to Federica to solve this issue
+
+By clicking on [intOGen-plus-dsl2](https://cloud.seqera.io/orgs/bbglabirb/workspaces/ALP_pipelines/launchpad/217132460501467?sourceWorkspaceId=97012242959019)
+you'll be able to launch the pipeline.
+
+![alt text](../assets/images/intogen-dsl2/intogen_seqera.png)
+
+Before launching the pipeline, some parameters need to be configured. Here a simple but complete list of
+useful parameters is explained.
+
+!!! warning "We highly recommend to keep the defaults for those parameters not discussed in this page."
+
+=== "General config section"
+
+    #### **Revision number**<!-- markdownlint-disable MD046 -->
+    
+    ![Revision number](../assets/images/intogen-dsl2/revision_number.png){ height="300" style="display: block; margin: 0 auto" }
+
+    By default, the **revision number** is linked to the stable tag of the pipeline. As of now - it's `2024.11-dsl2`. 
+    This can eventually be changed if a run is resumed or relaunched from the run section.
+
+    !!! note "Please be aware that changing this section may affect the `resume` option"
+
+    #### **Config profile**
+
+    ![Config profile](../assets/images/intogen-dsl2/config_profile.png){ height="300" style="display: block; margin: 0 auto" }
+
+    - `test` --> this is using the [CBIOP cohort](https://github.com/bbglab/intogen-plus-dsl2/blob/dev/DSL2/tests/data/pipeline/input/cbioportal_prad_broad/data_mutations_extended.txt) in the repo [optional]<!-- markdownlint-disable MD013 -->
+    - `test_full` --> this is using the full datasets of intogen [optional].
+    - `singularity` --> this is allowing the use of singularity for using the containers
+    - `irb` --> this is allocating the right resources and queue for the slurm executor in the IRBCluster
+
+    #### **Workflow run name**
+
+    ![Run name](../assets/images/intogen-dsl2/workflow_name.png){ height="300" style="display: block; margin: 0 auto" }
+
+    It's **mandatory** to write a meaningful name. Here follows some examples:
+
+    - If I am running a new combination optimization I would call the run: `optimization_combination`
+    - If I am running a FULL run with a new final version of intogen I would call it: `v3.0_ALL`
+    - If I am reproducing the v2024 run I would call it: `v2024_ALL`
+    - If I am running a specific cohort from an external collaborator I would call it: `v2024_EXT_COLLAB`
+
+    #### **Work directory**
+
+    ![work directory](../assets/images/intogen-dsl2/work_dir.png){ height="300" style="display: block; margin: 0 auto" }
+    
+    By default, the work directory is `/data/bbg/nobackup2/work/IntOGenDSL2/v2024/`.
+    For faster execution you can use the scratch partition in the cluster: `/scratch/bbg/work/IntOGenDSL2/v2025/<your-subfolder>`.
+    Replace `<your-subfolder>` with a meaningful name, such as the `Outdir` value from the next section, to avoid conflicts.
+    
+    !!! warning "Delete the work folder once the intogen run finishes successfully."
+    
+
+=== "Run parameters section"
+
+    #### **Input**<!-- markdownlint-disable MD046 -->
+
+    This parameter is read as a string, and it should be the absolute paths of the folder that openvariant will iterate
+    separated by a space. Here it follows an example:
+
+    ```sh
+    /path/to/datasets/for/intogen/input1 /path/to/datasets/for/intogen/input2 /path/to/datasets/for/intogen/input3
+    ```
+
+    !!! question "How do I prepare the input for IntOGen?"
+        Great question! Here the documentation where everything is explained: 
+        [intogen-plus.readthedocs](https://intogen-plus.readthedocs.io/en/v2024/usage.html#input)
+
+    #### **Outdir**
+
+    This parameter is where the output of intogen will be stored. By default we store
+    intermediate runs that might fail here:
+
+    ```sh
+    /data/bbg/nobackup2/scratch/intogen_dev_tests/dev-DSL2/v2024/<MeaningfulName>
+    ```
+
+    !!! note "It's important to add a meaningful name as a final directory output"
+        by default IntOGen will create a folder with a date where all the results will be stored. This although
+        requires an higher level of specificity in the top folder.
+
+        e.g. If I am running an external collab for LUNG data, I will add as an `outdir` parameter:
+        ```sh
+        /data/bbg/nobackup2/scratch/intogen_dev_tests/dev-DSL2/v2024/Lung_external_collab
+        ```
+        
+        The IntOGen pipeline will by default create a subdirectory with the date of the
+        launch where it will store all the files:
+        ```sh
+        /data/bbg/nobackup2/scratch/intogen_dev_tests/dev-DSL2/v2024/Lung_external_collab/20250423/
+        ```
+
+
+    Stable runs and releases are officially stored in a safer partition: 
+    ```sh
+    /data/bbg/datasets/intogen/output/runs
+    ```
+
+Once both those sections are completed we are safe to run the pipeline.
+
+### FAQs
+
+!!! question "The pipeline failed. How do I resume?"
+    In the [run tab](https://cloud.seqera.io/orgs/bbglabirb/workspaces/bbglab/watch) click on the three
+    dots on the right of your run and click `Resume`.
+
+- TBC
+
+## References
+
+- Federica Brando
+- Miguel Grau