Metadata-Version: 2.1
Name: cg-fluffy
Version: 0.4.1
Summary: NIPT analysis pipeline
Home-page: https://github.com/Clinical-Genomics/fluffy
Author: Jesper Eisfeldt
Author-email: jesper.eisfeldt@scilifelab.com
License: MIT
Description: 
        ![Build](https://github.com/Clinical-Genomics/fluffy/workflows/Build/badge.svg)
        [![codecov](https://codecov.io/gh/Clinical-Genomics/fluffy/branch/master/graph/badge.svg)](https://codecov.io/gh/Clinical-Genomics/fluffy)
        # FluFFyPipe
        NIPT analysis pipeline, using WisecondorX for detecting aneuplodies and large CNVs, AMYCNE for FFY and PREFACE for FF prediction (optional). FluFFYPipe produces a variety of output files, as well as a per batch csv summary.
        
        <p align="center">
        <img src="https://github.com/J35P312/FluFFyPipe/blob/master/logo/IMG_20200320_132001.jpg" width="400" height="400" >
        </p>
        
        # Run FluFFyPipe
        Run NIPT analysis:
        
            fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> analyse
        
        optionally, skip preface:
        
            fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> --skip_preface analyse
        
        All output will be written to the output folder, this output includes:
        
        ```
        bam files
        wisecondorX output
        tiddit coverage summary
        Fetal fraction estimation
        ```
        
        as well as a summary csv (per batch)
        
        the input folder is a project folder containing one folder per sample, each of these subfolders contain the fastq file(s).
        The samplesheet contains at least a "sampleID" column, the sampleID should match the subfolders in the input folder. The samplesheet may contain other columns, such as flowcell and index folder: such columns will be printed to the summary csv.
        
        Create a WisecondorX reference
        
            fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> reference
        
        samplesheet should contain atleast a "sampleID" column. All samples in the samplesheet will be used to construct the reference, visit the WisecondorX manual for more information.
        
        # Install FluFFyPipe
        FluFFyPipe requires python 3, slurm, slurmpy, and singularity, python-coloredlogs.
        
        First clone fluffypipe:
        
        `git clone https://github.com/Clinical-Genomics/fluffy`
        
        Install fluffy using pip
        
        cd fluffy
        
        `pip install -e .`
        
        Next download the FluFFyPipe singularity container
        
             singularity pull --name FluFFyPipe.sif shub://J35P312/FluFFyPipe
        
        copy the example config (found in example_config), and edit the variables.
        You will need to download/create the following files:
        
        	Reference fasta (indexed using bwa)
        
        	WisecondorX reference files (created using the --mkref mode)
        
        	PREFACE model file (optional)
        
        	blacklist bed file (used by wisecondorX)
        
        	FluFFyPipe singularity collection (singularity pull --name FluFFyPipe.sif shub://J35P312/FluFFyPipe)
        
Keywords: vcf,compression
Platform: UNKNOWN
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Unix
Classifier: Intended Audience :: Science/Research
Requires-Python: >=3.6.0
Description-Content-Type: text/markdown
