Package: wespipeline
WespipelineAn implementation of a whole exome analysis pipeline usingLuigi <https://github.com/spotify/luigi/>_ for workflow management... figure::https://raw.githubusercontent.com/janchorizo/wespipeline/master/docs/steps.png:alt: Steps Logo
:align: centerThis package provides with the implementation of tasks for executing partial or complete variant calling
analysis with the advantages of having a workflow manager: dependency resolution, execution planner,
modularity, monitoring and historic.Documentation for the latest version is being hosted byreadthedocs <https://wespipeline.readthedocs.io/en/latest/>_Installation
^^^^^^^^^^^^
Wespipeline is available through pip, conda and manual installation. Install it from the package repositoriespip3 install wespipelineconda install -c jancho wespipeline, or download the project and build from source:git clone https://github.com/Janchorizo/wespipeline.git && cd wespipeline && python3 setup.py install.Notice that executing the analysis will involve different additional dependencies depending on the steps that executed and the
parameters set for these. All possible are cited below and can be downloaded with the Anaconda distribution:Secuence retrieval : Sra Toolkit, FastqcReference genome retrieval : No needed dependencySecuence alignment : BwaAlignment processing : Bwa Samtools,Variant calling : Freebayes, Varscan, Gatk, DeepvariantVariant calling evaluation : Vcf toolsIn addition to the dependencies, conda can be used for installing thewespipelinepackage. An example for
installing the miniconda distribution, the package and the dependencies is:.. code-block:: bashwgethttps://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh-O ~/miniconda.sh
bash ~/miniconda.sh -b -p $HOME/miniconda
export PATH="$HOME/miniconda/bin:$PATH"
source $HOME/miniconda/bin/activate &&conda config --add channels bioconda &&conda config --add channels conda-forge &&conda config --add channels jancho &&conda install -y samtools &&conda install -y bwa &&conda install -y picard &&conda install -y platypus-variant &&conda install -y varscan &&conda install -y freebayes &&conda install -y fastqc &&conda install -y sra-tools &&conda install -y wespipelinerm ~/miniconda.shGetting started
^^^^^^^^^^^^^^^Installing or downloading the package will provide with a higher level task per step of the
analysis, each of which can be executed in a similar fashion to other Luigi tasks.Each of the six steps have a higher level task that can be scheduled in a similar fashion
to other Luigi tasks:.. code-block:: bashpython3 -m luigi --module wespipeline.<module> <Taskname> --<Taskname>-param valueDownload the sequences using the NCBI accession number... code-block:: bashpython3 -m luigi --module wespipeline.fastq FastqRetrieval \
	--FastqRetrieval-paired-end true \
	--FastqRetrieval-accession-number SRR9209557 \
	--FastqRetrieval-create-report trueOr an external url... code-block:: bashpython3 -m luigi --module wespipeline.fastq FastqRetrieval \
	--FastqRetrieval-paired-end true \
	--FastqRetrieval-compressed false \
	--FastqRetrieval-accession-number SRR9209557 \
	--FastqRetrieval-create-report trueDownload the reference genome and create a report using FastqC... code-block:: bashpython3.6 -m luigi --module tasks.reference ReferenceRetrieval 
	--workers 3 \
	--ReferenceGenome-ref-url ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit \
	--ReferenceGenome-from2bit True \
	--GlobalParams-base-dir ./tfm_experiment \
	--GlobalParams-log-dir .logs \
	--GlobalParams-exp-name hg19Or run the whole analysis, specifying the parameters for each of the steps... code-block:: bashpython3 -m luigi --module tasks.vcf VariantCalling 
	--workers 3 
	--VariantCalling-use-platypus true 
	--VariantCalling-use-freebayes true 
	--VariantCalling-use-samtools false 
	--VariantCalling-use-gatk false 
	--VariantCalling-use-deepcalling false 
	--AlignProcessing-cpus 6 
	--FastqAlign-cpus 6 
	--FastqAlign-create-report True 
	--GetFastq-gz-compressed True 
	--GetFastq-fastq1-url ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/NIST7035_TAAGGCGA_L001_R1_001.fastq.gz 
	--GetFastq-fastq2-url ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/NIST7035_TAAGGCGA_L001_R2_001.fastq.gz 
	--GetFastq-from-ebi False 
	--GetFastq-paired-end True 
	--ReferenceGenomeRetrieval-ref-url ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.2bit --ReferenceGenomeRetrieval-from2bit True 
	--GlobalParams-base-dir ./tfm_experiment 
	--GlobalParams-log-dir .logs 
	--GlobalParams-exp-name hg19Tasks implemented
^^^^^^^^^^^^^^^^^+-----------------+----------------------------+
| Module          | Task                       |
+=================+============================+
| reference       | ReferenceGenomeRetrieval   |
+-----------------+----------------------------+
| fastq           | FastqRetrieval             |
+-----------------+----------------------------+
| align           | FastqAlignment             |
+-----------------+----------------------------+
| processalign    | FastqProcessing            |
+-----------------+----------------------------+
| variantcalling  | VariantCalling             |
+-----------------+----------------------------+
| processalign    |  VariantProcessing         |
+-----------------+----------------------------+Acknowledgements
^^^^^^^^^^^^^^^^Special thanks to professor Luis Antonio Miguel Quintales for all the guidance and help provided during the
development of this project.