Nextflow pipeline to study intra-tumoral heterogeneity through subclonality reconstruction, using HATCHet, DeCiFer and clonEvol. PIPELINE IN DEVELOPMENT.
- 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:
You can avoid installing all the external software by only installing Docker. See the IARC-nf repository for more information.
| Type | Description |
|---|---|
| --bam_folder | Folder containing BAM files to pass to HATCHet |
| Name | Example value | Description |
|---|---|---|
| --ref | /whole/path/to/genome.fa | Reference genome in fasta format |
| --correspondance | TN_pairs.txt | Tabulated file containing two columns: tumor and normal bam names |
| Name | Default value | Description |
|---|---|---|
| --cpu | 1 | Number of cpu to use |
| --config | null | Use custom configuration file |
| --mem | 4 | Size of memory used in GB |
| --output_folder | . | Path to output folder |
| --samtools_folder | /usr/bin/ | samtools installation dir |
| --bcftools_folder | /usr/bin/ | bcftools installation dir |
| --hatchet_folder | /usr/bin/ | hatchet installation dir |
| --bnpy_folder | /usr/bin/ | bnpy installation dir |
Flags are special parameters without value.
| Name | Description |
|---|---|
| --help | Display help |
nextflow run iarcbioinfo/ITH_pipeline --bam_folder bam_folder/ --ref genome.fa --correspondance pairs.txt --cpu 24 --samtools_folder ~/bin/samtools-1.7 --bcftools_folder ~/bin/bcftools-1.7 --hatchet_folder ~/bin/hatchet --bnpy_folder ~/bin/bnpy-dev
| Type | Description |
|---|---|
| ...... | ...... |
...
| Name | Description | |
|---|---|---|
| Tiffany Delhomme | delhommet@students.iarc | Developer to contact for support |