Nextflow pipeline to run tumor subclone detection software DPclust, perform postprocessing and run mutationTimeR to date amplifications
- 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
| 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 |
| 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 are special parameters without value.
| Name | Description |
|---|---|
| --help | Display help |
nextflow run iarcbioinfo/DPclust-nf [-with-docker] [OPTIONS]
| 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 |
| Name | Description | |
|---|---|---|
| Nicolas Alcala* | [email protected] | Developer to contact for support |