Package: cg-fluffy
FluFFyPipeNIPT 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.Run FluFFyPipeRun NIPT analysis, using a previously comnputed reference:fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> --analyseRun 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-refoptionally, skip preface:fluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> --skip_preface --analyseAll output will be written to the output folder, this output includes:bam files
wisecondorX output
tiddit coverage summary
Fetal fraction estimationas 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 SampleNameCreate a WisecondorX referencefluffy --sample <samplesheet>  --project <input_folder> --out <output_folder> --referencesamplesheet 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.Optional fluffy parameters:Analysis mode:
	--dry_run - run the pipeline without generating files
	-l	-	add paramters to the slurm header of the script, should be given on the following format parameter:value
			example: qos:high 

Reference mode:
	--dry_run - run the pipeline without generating files

Rerun mode:
	--dry_run - run the pipeline without generating filesTroubleshooting and rerunThere are three statuses of the fluffy pipeline:
running, complete, and failedThe status of a fluffy run is found in the<output_folder>/analysis_status.jsonThe status of all jobs are listed in<output_folder>/sacct/fluffy_<date>.log.statusWhere  is the timepoint when the jobs were submitted
Use grep to find the failed jobs:grep -v COMPLETE <output_folder>/sacct/fluffy_<date>.log.statusThe output logs are stored in:<output_folder>/logsBefore continuing, you may want to generate the summary csv for all completed cases:bash <output_folder>/scripts/summarizebatch-<hash>where  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 rerunInstall FluFFyPipeFluFFyPipe requires python 3, slurm, slurmpy, and singularity, python-coloredlogs.fluffy may be installed using pip:pip install fluffy-cgalternatively, fluffy is cloned and installed from github:
git clonehttps://github.com/Clinical-Genomics/fluffycd fluffy
pip install -e .Next download the FluFFyPipe singularity containersingularity pull library://jeisfeldt/default/fluffy:sha256.dbef92cd5eab8558c2729f73a191d73a7576a24e9bb44dde7372c0cd405c4ef6copy 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)