Nextflow Config File Parameters
| Field | Required | Type | Description |
|---|---|---|---|
| dataset_id | yes | string | Boutros Lab dataset id |
| blcds_registered_dataset | yes | boolean | Affirms if dataset should be registered in the Boutros Lab Data registry. Default value is false. |
| algorithm | yes | list | List containing a combination of SV callers delly, manta. List can contain a single caller of choice. |
| reference_fasta | yes | path | Absolute path to the reference genome FASTA file. The reference genome is used by Delly for structural variant calling. GRCh37 - /hot/ref/reference/GRCh37-EBI-hs37d5/hs37d5.fa, GRCh38 - /hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta |
| exclusion_file | yes | path | Absolute path to the Delly reference genome exclusion file utilized to remove suggested regions for structural variant calling. GRCh37 - /hot/ref/tool-specific-input/Delly/GRCh37-EBI-hs37d/human.hs37d5.excl.tsv, GRCh38 - /hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv |
| map_qual | yes | integer | Minimum paired-end (PE) mapping quality (MAPQ) for Delly. Default set to 20. |
| min_clique_size | yes | integer | Minimum number of supporting PE or split-read (SR) alignments required for a clique to be identified as a structural variant by Delly. Adjust this parameter to control the sensitivity and specificity of Delly variant calling. Default set to 5. |
| mad_cutoff | yes | integer | Insert size cutoff, median+s*MAD (deletions only) for Delly. Default set to 15. |
| save_intermediate_files | yes | boolean | Optional parameter to indicate whether intermediate files will be saved. Default value is false. |
| output_dir | yes | path | Absolute path to the directory where the output files to be saved. |
| work_dir | no | path | Path of working directory for Nextflow. When included in the sample config file, Nextflow intermediate files and logs will be saved to this directory. With ucla_cds, the default is /scratch and should only be changed for testing/development. Changing this directory to /hot or /tmp can lead to high server latency and potential disk space limitations, respectively. |
| verbose | yes | boolean | If set to true, the values of input channels will be printed, can be used for debugging |
docker_container_registry |
optional | string | Registry containing tool Docker images. Default: ghcr.io/uclahs-cds |
An example of the NextFlow Input Parameters Config file can be found here.