Nextflow pipeline to discover ecDNA in cancer genomes.
#using a tn_pairs file
nextflow run iarcbioinfo/ampliconarchitect-nf -r v1.0 \
-profile singularity --tumor_file tumor_file.txt \
--cram_dir $PWD/CRAM \
--moseklm_license mosek.lic --aa_repo_dir GRCh38 \
--output_folder ecDNA_public1
#testing a small fake run
nextflow run iarcbioinfo/ampliconarchitect-nf -r v1.0 \
--tumor_file test/tumor_file.txt \
--cram_dir test/cram \
--moseklm_license test/mosic_license/mosic.license \
--aa_repo_dir test/amplicon_repo --debug true
Obtain license file mosek.lic (https://www.mosek.com/products/academic-licenses/ or https://www.mosek.com/try/).
To run amplicon architect is necessary to download the Amplicon Architect repository from here, currently we have tested this nextflow pipeline with GRCh38 genome built.
You can avoid installing all the external software by only installing Docker or singularity. See the IARC-nf repository for more information.
| Parameter | Description |
|---|---|
| --cram_dir | Directory containing all BAM/CRAM files |
| --tumor_file | File containing list of tumor CRAM files to be processed |
| --moseklm_license | License for mosek program [mosic.license] |
| --aa_repo_dir | directory containing the Amplicon Architect repository [See above] |
| Parameter | Description |
|---|---|
| --output_folder | name of output folder [def:amplicon_results] |
| --cpu | Number of CPUs[def:1] |
| --mem | Max memory [def:8Gb] |
| --debug | enable debuging of the pipeline |
A text file tabular separated, with the following header:
id cram
sample1_T1 sample1_T.cram
sample2_T1 sample2_T.cram
sample3_T1 sample3_T.cram
├── amplicon_classes # amplicon classified
│ └── all_amplicons_classification_bed_files # amplicon in genomic coordiantes
├── amplicon_predictions # Amplicon architect predictions
│ ├── S00016_T.aa
│ ├── S01493_T.aa
│ ├── S01501_T.aa
├── amplified_intervals #Selected seeds per sample
├── cnvkit #CNVkit copyNumber segments
│ ├── S00016_T
│ ├── S01493_T
│ ├── S01501_T
│ ├── S01502_T
└── nf-pipeline_info # Nextflow logs
The first time that the container is built from the docker image, the TMPDIR should be defined in a non parallel file-system, you can set this like:
export TMPDIR=/tmp
| Name | Description | |
|---|---|---|
| Matthieu Foll* | [email protected] | Developer to contact for support (link to specific gitter chatroom) |
| Alex Di Genova | [email protected] | Developer |