Metadata-Version: 2.1
Name: cg-fluffy
Version: 0.8.2
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, using a previously comnputed reference:
        
            fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> analyse
            
        Run NIPT analysis, using an internally computed reference (i.e the reference is built using all samples listed in samplesheet):
        
            fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> analyse --batch-ref
        
        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 and multiqc html (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.
        If the samplesheet contains a SampleName column, fluffy will name the output according to SampleName
        
        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.
        
        # Troubleshooting and rerun
        There are three statuses of the fluffy pipeline:
        running, complete, and failed
        
        The status of a fluffy run is found in the
        
        	<output_folder>/analysis_status.json
        	
        The status of all jobs are listed in
        
        	<output_folder>/sacct/fluffy_<date>.log.status
        	
        Where <date> is the timepoint when the jobs were submitted
        Use grep to find the failed jobs:
        	
        	grep -v COMPLETE <output_folder>/sacct/fluffy_<date>.log.status
        	
        The output logs are stored in:
        
        	 <output_folder>/logs
        
        Before continuing, you may want to generate the summary csv for all completed cases:
        
        	bash <output_folder>/scripts/summarizebatch-<hash>
        
        where <hash> is a randomly generated string.
        	
        use the rerun module to rerun failed fluffy analyses:
        
        	fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> --skip_preface rerun
        	
         
        # Install FluFFyPipe
        FluFFyPipe requires python 3, slurm, slurmpy, and singularity, python-coloredlogs.
        
        fluffy may be installed using pip:
        
        	pip install fluffy-cg
        
        alternatively, fluffy is cloned and installed from github:
        	git clone https://github.com/Clinical-Genomics/fluffy
        	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 reference 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
