🐍 clinical-genomics-uppsala/marple 🕵️‍♀️

Twist Cancer inherited hg38 hydra pipelines

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https://marple-rd-tc.readthedocs.io/en/latest/

This ReadMe is only a brief introduction, please refer to ReadTheDocs for the latest documentation.

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💬 Introduction

This pipeline is created to run on Illumina data from a custom Twist Inherited Cancer panel, designed at Clinical Genomics Uppsala.

🧑‍⚖️ Rule Graph

✅ Testing

The workflow repository contains a small test dataset (:exclamation: Todo: as of now dry-run only) .tests/integration which can be run like so:

$ cd .tests/integration
$ snakemake -n -s ../../workflow/Snakefile --configfiles ../../config/config.yaml config.yaml --config sequenceid="990909_test" PATH_TO_REPO=/folder/containing/marple_rd_tc/

NOTE: If using the variable PATH_TO_REPO in the config-file this need to be defined in the commandline

🚀 Usage

To use this run this pipeline sample.tsv, units.tsv, resources.yaml, and config.yaml files need to be available in the current directory (or otherwise specified in config.yaml). You always need to specify the config-file and sequenceid variable in the command. To run the pipeline:

$ snakemake --profile snakemakeprofile --configfile config.yaml --config sequenceid="990909_test" -s /path/to/marple_rd_tc/workflow/Snakefile --config PATH_TO_REPO=/folder/containing/marple_rd_tc/

NOTE: If using the variable PATH_TO_REPO in the config this need to be defined in the commandline

📚 Output files

The following output files are located in Results/-folder:

File	Format	Description
multiqc_DNA.html	html	Aggregated QC values for entire sequence run, open in browser
{sample}_{sequenceid}/{sample}_{sequenceid}.xlsx	xlsx	Excel file with QC stats (primarily coverage) for each sample
{sample}_{sequenceid}/{sample}_{sequenceid}.bam	bam	Deduplicated alignment file
{sample}_{sequenceid}/{sample}_{sequenceid}.bam.bai	bai	Index for alignment file
{sample}_{sequenceid}/{sample}_{sequenceid}.vcf.gz	vcf.gz	Compressed VCF-file decomposed, normalized and annotated with vep
{sample}_{sequenceid}/{sample}_{sequenceid}.vcf.gz.tbi	tbi	Index for variant file
{sample}_{sequenceid}/{sample}_{sequenceid}.genome.vcf.gz	genome.vcf.gz	Compressed VCF-file for all positions in the design, not decomposed nor normalized
{sample}_{sequenceid}/{sample}_{sequenceid}.genome.vcf.gz.tbi	tbi	Index for genome VCF-file
{sample}_{sequenceid}/{sample}_{sequenceid}_exomedepth_SV.txt	txt	Nexus SV text file with structural variants from Exomedepth
{sample}_{sequenceid}/{sample}_{sequenceid}_exomedepth.aed	aed	aed text file with structural variants from Exomedepth
{sequenceid}_config.yaml	yaml	yaml config-file with programversion and extra settings used