.. _`rna-count-salmon (✓ production)`:

RNA-COUNT-SALMON (✓ PRODUCTION)
===============================

Version: 1.0.0
Tags: Fastq / Quantification / Cleaning / Flamingo / Automated

This is the fully automated pipeline for Salmon quantification on Flamingo.
No config, no design, no time wasted.

« A good pipeline has no documentation » Someone at BiGR


.. role:: bash(code)
  :language: bash

Pipeline dependencies
---------------------

This pipeline requires the following packages to be run. Any other additional requirements are being installed dynamically.

Conda:
  
  * conda-forge::python ==3.9.2
  
  * conda-forge::git ==2.30.2
  
  * conda-forge::jinja2 ==2.11.3
  
  * conda-forge::pygraphviz ==1.7
  
  * conda-forge::flask ==1.1.2
  
  * conda-forge::pandas ==1.2.3
  
  * conda-forge::zlib ==1.2.11
  
  * conda-forge::openssl ==1.1.1k
  
  * conda-forge::networkx ==2.5.1
  
  * bioconda::snakemake ==6.1.1
  
  * conda-forge::black ==20.8b1
  
  * conda-forge::singularity ==3.7.1
  
  * conda-forge::mamba ==0.9.2
  


Additionally, the following prerequisites are non-optional:


* None. Everything is on Flamingo already.




Input files
-----------

Please find below the list of required input files:


* Several **paried** Fastq files.



Output files
------------

Please find below the list of expected output files:


* Quantified reads

* MultiQC report




Notes
-----

This pipeline handles iRODS copies.

Fastp -> Salmon -> MultiQC.





Installation
------------

While installing the workflow, you may run the following commands (order matters):

.. list-table::
  :widths: 10 80
  :header-rows: 1
  :align: left

  * - Case
    - Command line
  * - none
    - .. code-block:: bash 

        # No installation needed.



Testing
-------

In order to test the pipeline, you may try the following commands:

.. list-table::
  :widths: 10 80
  :header-rows: 1
  :align: left

  * - Case
    - Command line
  * - quick-test
    - .. code-block:: bash 

        bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/salmon_quant/test.sh
  * - verbose-test
    - .. code-block:: bash 

        bash -x /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/salmon_quant/test.sh




Preparation
-----------

In order to prepare a run, you may try the following commands:

.. list-table::
  :widths: 10 80
  :header-rows: 1
  :align: left

  * - Case
    - Command line
  * - none
    - .. code-block:: bash 

        # No preparation, everything is available.



Execution
---------

In order to execute the pipeline, you may run the following commands:

.. list-table::
  :widths: 10 80
  :header-rows: 1
  :align: left

  * - Case
    - Command line(s)
  * - hg19
    - .. code-block:: bash 

        bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/salmon_quant/run.sh hg19
  * - hg38
    - .. code-block:: bash 

        bash /mnt/beegfs/pipelines/snakemake-wrappers/bigr_pipelines/salmon_quant/run.sh hg38