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| 1 | +# nf-core/oncorefiner pipeline parameters |
| 2 | + |
| 3 | +Customizable post-processing and extension layer built on top of Oncoanalyser that adapts its outputs to clinical and operational needs, adds missing analyses, and ensures flexibility for evolving standards while retaining Oncoanalyser robust core |
| 4 | + |
| 5 | +## Input/output options |
| 6 | + |
| 7 | +Define where the pipeline should find input data and save output data. |
| 8 | + |
| 9 | +| Parameter | Description | Type | Default | Required | Hidden | |
| 10 | +|-----------|-----------|-----------|-----------|-----------|-----------| |
| 11 | +| `input` | Path to comma-separated file containing information about the samples in the experiment. <details><summary>Help</summary><small>You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/oncorefiner/usage#samplesheet-input).</small></details>| `string` | | True | | |
| 12 | +| `outdir` | The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure. | `string` | | True | | |
| 13 | +| `email` | Email address for completion summary. <details><summary>Help</summary><small>Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.</small></details>| `string` | | | | |
| 14 | +| `multiqc_title` | MultiQC report title. Printed as page header, used for filename if not otherwise specified. | `string` | | | | |
| 15 | + |
| 16 | +## Reference genome options |
| 17 | + |
| 18 | +Reference genome related files and options required for the workflow. |
| 19 | + |
| 20 | +| Parameter | Description | Type | Default | Required | Hidden | |
| 21 | +|-----------|-----------|-----------|-----------|-----------|-----------| |
| 22 | +| `genome` | Name of iGenomes reference. <details><summary>Help</summary><small>If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. <br><br>See the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.</small></details>| `string` | | | | |
| 23 | +| `fasta` | Path to FASTA genome file. <details><summary>Help</summary><small>This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.</small></details>| `string` | | | | |
| 24 | +| `fai` | Path to FASTA genome index file. <details><summary>Help</summary><small>If none provided, will be generated automatically from the FASTA reference</small></details>| `string` | | | | |
| 25 | +| `igenomes_ignore` | Do not load the iGenomes reference config. <details><summary>Help</summary><small>Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`.</small></details>| `boolean` | | | True | |
| 26 | +| `igenomes_base` | The base path to the igenomes reference files | `string` | s3://ngi-igenomes/igenomes/ | | True | |
| 27 | + |
| 28 | +## Annotation options |
| 29 | + |
| 30 | +Annotation related files and options required for the workflow. |
| 31 | + |
| 32 | +| Parameter | Description | Type | Default | Required | Hidden | |
| 33 | +|-----------|-----------|-----------|-----------|-----------|-----------| |
| 34 | +| `vep_cache_version` | Specify the version of the VEP cache provided to the `--vep_cache` option. | `integer` | 112 | | | |
| 35 | +| `vep_cache` | Path to vep's cache directory. <details><summary>Help</summary><small>If no directory path is passed, vcf files will not be annotated by vep.</small></details>| `string` | | | | |
| 36 | +| `vep_plugin_files` | Databases used by both named and custom plugins to annotate variants. <details><summary>Help</summary><small>Path to a file containing the absolute paths to databases and their indices used by VEP's custom and named plugins resources defined within the vcfanno toml file. One line per resource.</small></details>| `string` | | | | |
| 37 | +| `vcfanno_extra` | Path to a VCF file containing annotations. <details><summary>Help</summary><small>Can be used to supply case-specific annotations in addition to those provided using --vcfanno_resources</small></details>| `string` | | | | |
| 38 | +| `vcfanno_resources` | Path to a file containing the absolute paths to resources defined within the vcfanno toml file. One line per resource. <details><summary>Help</summary><small>If no file is passed, default configurations will be used according to genome build within the context of the pipeline.</small></details>| `string` | | | | |
| 39 | +| `vcfanno_toml` | Path to the vcfanno toml file. <details><summary>Help</summary><small>If no toml is passed, default configurations will be used according to genome build within the context of the pipeline.</small></details>| `string` | | | | |
| 40 | +| `vcfanno_lua` | Path to the vcfanno lua file. <details><summary>Help</summary><small>Custom operations file (lua). For use when the built-in ops don't supply the needed reduction.</small></details>| `string` | | | | |
| 41 | +| `svdb_query_dbs` | Databases used for structural variant annotation in vcf format. <details><summary>Help</summary><small>Path to comma-separated file containing information about the databases used for structural variant annotation.</small></details>| `string` | | | | |
| 42 | + |
| 43 | +## Institutional config options |
| 44 | + |
| 45 | +Parameters used to describe centralised config profiles. These should not be edited. |
| 46 | + |
| 47 | +| Parameter | Description | Type | Default | Required | Hidden | |
| 48 | +|-----------|-----------|-----------|-----------|-----------|-----------| |
| 49 | +| `custom_config_version` | Git commit id for Institutional configs. | `string` | master | | True | |
| 50 | +| `custom_config_base` | Base directory for Institutional configs. <details><summary>Help</summary><small>If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.</small></details>| `string` | https://raw.githubusercontent.com/nf-core/configs/master | | True | |
| 51 | +| `config_profile_name` | Institutional config name. | `string` | | | True | |
| 52 | +| `config_profile_description` | Institutional config description. | `string` | | | True | |
| 53 | +| `config_profile_contact` | Institutional config contact information. | `string` | | | True | |
| 54 | +| `config_profile_url` | Institutional config URL link. | `string` | | | True | |
| 55 | + |
| 56 | +## Generic options |
| 57 | + |
| 58 | +Less common options for the pipeline, typically set in a config file. |
| 59 | + |
| 60 | +| Parameter | Description | Type | Default | Required | Hidden | |
| 61 | +|-----------|-----------|-----------|-----------|-----------|-----------| |
| 62 | +| `version` | Display version and exit. | `boolean` | | | True | |
| 63 | +| `publish_dir_mode` | Method used to save pipeline results to output directory. (accepted: `symlink`\|`rellink`\|`link`\|`copy`\|`copyNoFollow`\|`move`) <details><summary>Help</summary><small>The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.</small></details>| `string` | copy | | True | |
| 64 | +| `email_on_fail` | Email address for completion summary, only when pipeline fails. <details><summary>Help</summary><small>An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.</small></details>| `string` | | | True | |
| 65 | +| `plaintext_email` | Send plain-text email instead of HTML. | `boolean` | | | True | |
| 66 | +| `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | `string` | 25.MB | | True | |
| 67 | +| `monochrome_logs` | Do not use coloured log outputs. | `boolean` | | | True | |
| 68 | +| `hook_url` | Incoming hook URL for messaging service <details><summary>Help</summary><small>Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.</small></details>| `string` | | | True | |
| 69 | +| `multiqc_config` | Custom config file to supply to MultiQC. | `string` | | | True | |
| 70 | +| `multiqc_logo` | Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file | `string` | | | True | |
| 71 | +| `multiqc_methods_description` | Custom MultiQC yaml file containing HTML including a methods description. | `string` | | | | |
| 72 | +| `validate_params` | Boolean whether to validate parameters against the schema at runtime | `boolean` | True | | True | |
| 73 | +| `pipelines_testdata_base_path` | Base URL or local path to location of pipeline test dataset files | `string` | https://raw.githubusercontent.com/Clinical-Genomics/test-datasets/refs/heads/oncorefiner/ | | True | |
| 74 | +| `trace_report_suffix` | Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss. | `string` | | | True | |
| 75 | +| `help` | Display the help message. | `['boolean', 'string']` | | | | |
| 76 | +| `help_full` | Display the full detailed help message. | `boolean` | | | | |
| 77 | +| `show_hidden` | Display hidden parameters in the help message (only works when --help or --help_full are provided). | `boolean` | | | | |
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