=================
All Available Modules
=================
Below are all available modules in the current release of Omics Pipe in alphabetical order. When creating 
a custom pipeline, you can choose from these modules or create your own. 

.. automodule:: omics_pipe.modules.annotate_peaks
	:members:
	
.. automodule:: omics_pipe.modules.annotate_variants
	:members:
	
.. automodule:: omics_pipe.modules.bowtie
	:members:
	
.. automodule:: omics_pipe.modules.BreastCancer_RNA_report
	:members:
	
.. automodule:: omics_pipe.modules.bwa
	:members:
	
.. automodule:: omics_pipe.modules.call_variants
	:members:
	
.. automodule:: omics_pipe.modules.ChIP_trim
	:members:
	
.. automodule:: omics_pipe.modules.cuffdiff
	:members:	
	
.. automodule:: omics_pipe.modules.cuffdiff_miRNA
	:members:
	
.. automodule:: omics_pipe.modules.cufflinks
	:members:	
	
.. automodule:: omics_pipe.modules.cufflinks_miRNA
	:members:	
	
.. automodule:: omics_pipe.modules.cufflinks_ncRNA
	:members:	
	
.. automodule:: omics_pipe.modules.cuffmerge
	:members:
	
.. automodule:: omics_pipe.modules.cuffmerge_miRNA
	:members:

.. automodule:: omics_pipe.modules.cuffmergetocompare
	:members:
	
.. automodule:: omics_pipe.modules.cuffmergetocompare_miRNA
	:members:	
	
.. automodule:: omics_pipe.modules.custom_R_report
	:members:	
	
.. automodule:: omics_pipe.modules.cutadapt_miRNA
	:members:
	
.. automodule:: omics_pipe.modules.fastq_length_filter_miRNA
	:members:
	
.. automodule:: omics_pipe.modules.fastqc
	:members:
	
.. automodule:: omics_pipe.modules.fastqc_miRNA
	:members:
	
.. automodule:: omics_pipe.modules.filter_variants
	:members:

.. automodule:: omics_pipe.modules.find_motifs
	:members:

.. automodule:: omics_pipe.modules.fusion_catcher
	:members:
	
.. automodule:: omics_pipe.modules.GATK_preprocessing_WES
	:members:
	
.. automodule:: omics_pipe.modules.GATK_preprocessing_WGS
	:members:	
	
.. automodule:: omics_pipe.modules.GATK_variant_discovery
	:members:

.. automodule:: omics_pipe.modules.GATK_variant_filtering
	:members:
	
.. automodule:: omics_pipe.modules.homer_peaks
	:members:
	
.. automodule:: omics_pipe.modules.htseq
	:members:	
	
.. automodule:: omics_pipe.modules.htseq_gencode
	:members:	
	
.. automodule:: omics_pipe.modules.htseq_miRNA
	:members:	
	
.. automodule:: omics_pipe.modules.intogen
	:members:	
	
.. automodule:: omics_pipe.modules.macs
	:members:	
	
.. automodule:: omics_pipe.modules.mutect
	:members:	
	
.. automodule:: omics_pipe.modules.peak_track
	:members:	
	
.. automodule:: omics_pipe.modules.picard_mark_duplicates
	:members:	
	
.. automodule:: omics_pipe.modules.read_density
	:members:	
	
.. automodule:: omics_pipe.modules.RNAseq_QC
	:members:	
	
.. automodule:: omics_pipe.modules.RNAseq_report
	:members:	
	
.. automodule:: omics_pipe.modules.RNAseq_report_counts
	:members:	
	
.. automodule:: omics_pipe.modules.RNAseq_report_tuxedo
	:members:	
	
.. automodule:: omics_pipe.modules.rseqc
	:members:		

.. automodule:: omics_pipe.modules.snpir_variants
	:members:
	
.. automodule:: omics_pipe.modules.star
	:members:
	
.. automodule:: omics_pipe.modules.star_piRNA
	:members:

.. automodule:: omics_pipe.modules.TCGA_download
	:members:
	
.. automodule:: omics_pipe.modules.tophat
	:members:
	
.. automodule:: omics_pipe.modules.tophat_miRNA
	:members:
	
.. automodule:: omics_pipe.modules.tophat_ncRNA
	:members: