Nextflow pipelines to run DPclust on sequencing data
Description
Nextflow pipeline to run tumor subclone detection software DPclust, perform postprocessing and run mutationTimeR to date amplifications
Dependencies
This pipeline is based on nextflow. As we have several nextflow pipelines, we have centralized the common information in the IARC-nf repository. Please read it carefully as it contains essential information for the installation, basic usage and configuration of nextflow and our pipelines.
External software:
DPclust. R package to cluster mutations to detect tumor subclones
dpclust3p. R package with useful functions to format DPclust inputs
MutationTimeR. R package to time amplification events
Input
Type
Description
CNV_file
Path to tab-separated file with copy number variants for all samples, in PURPLE format (see e.g. our purple-nf pipeline)
CNV_summary_file
Path to tab-separated file with copy number summary for all samples (in PURPLE output format)
input_file
Path to Input file (tab-separated values) with 4 columns: sampleID, vcf, normal, and tumor
Parameters
Optional
Name
Default value
Description
--vcf_folder
.
Path to folder with variants for all samples in VCF format
--bam_folder
.
Path to folder with BAM/CRAM files for tumor and normal samples
--output_folder
.
Path to output folder
--cpu
2
Number of cpus used
--mem
8
Memory used in Gb
--ext
cram
Extension of alignment files, cram or bam
Flags
Flags are special parameters without value.
Name
Description
--help
Display help
Usage
nextflow run iarcbioinfo/DPclust-nf [-with-docker] [OPTIONS]
Output
Type
Description
DPclust_inputs
Folder with inputs to DPclust formatted using dpclust3p: a folder for each sample with a DPmasterfile summarizing the files necessary to run DPclust, formatted CNVs and allele frequency tables
results/DPclust
Folder with outputs from DPclust: a folder for each sample with the location (CCF and number of alterations) of each subclone
results/MutationTimeR
Folder with results from mutationtimeR: timing of CNVs and SNVs
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