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-.. _home-page-moptail:
-
-*******************
-MOP_TAIL
-*******************
-
-.. autosummary::
-   :toctree: generated
-
-This pipeline takes as input the output from MOP_PREPROCESS: basecalled fast5 reads, together with their respective fastq files, alignment and assignment read ID to gene/transcript. It outputs the estimation of poly(A) tail length at read level provided by **Tailfindr**, **Nanopolish** or both. Tailfinr can be run using three modes: standard, for Nano3P-seq protocol with R9 chemistry and Nano3P-seq protocol with R10 chemistry.
-
-.. image:: ../img/flow_tail.png
-  :width: 600
-  :alt: mop_tail graph
-
-
-Input Parameters
-======================
-
-The input parameters are stored in yaml files like the one represented here:
-
-.. literalinclude:: ../mop_tail/params.yaml
-   :language: yaml
-
-
-
-How to run the pipeline
-=============================
-Before launching the pipeline,user should:
-
-1. Decide which containers to use - either docker or singularity **[-with-docker / -with-singularity]**.
-2. Fill in both **params.config** and **tools_opt.tsv** files.
-
-To launch the pipeline, please use the following command:
-
-.. code-block:: console
-
-   nextflow run mop_tail.nf -params-file params.yaml  -with-singularity > log.txt
-
-
-You can run the pipeline in the background adding the nextflow parameter **-bg**:
-
-.. code-block:: console
-
-   nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg > log.txt
-
-You can change the parameters either by changing **params.config** file or by feeding the parameters via command line:
-
-.. code-block:: console
-
-   nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg --output test2 > log.txt
-
-
-You can specify a different working directory with temporary files:
-
-.. code-block:: console
-
-   nextflow run mop_tail.nf -params-file params.yaml -with-singularity -bg -w /path/working_directory > log.txt
-
-
-Results
-====================
-
-Several folders are created by the pipeline within the output directory specified by the **output** parameter:
-
-1. NanoPolish: contains the output of *nanopolish* tool.
-2. Tailfindr: contains the output of *tailfindr* tool.
-3. PolyA_final: contains the txt files with the combined results (i.e. predicted polyA sizes). Here an example of a test:
-
-.. code-block:: console
-
-   "Read name"	"Tailfindr"	"Nanopolish"	"Gene Name"
-   "013a5dde-9c52-4de1-83eb-db70fb2cd130"	52.16	49.39	"YKR072C"
-   "01119f62-ca68-458d-aa1f-cf8c8c04cd3b"	231.64	274.28	"YDR133C"
-   "0154ce9c-fe6b-4ebc-bbb1-517fdc524207"	24.05	24.24	"YFL044C"
-   "020cde28-970d-4710-90a5-977e4b4bbc46"	41.27	56.79	"YGL238W"
-
-If both programs are run, an additional plot that shows the correlation of their results is generated.
-
-.. image:: ../img/mod_corr.png
-  :width: 400