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dxapp.json
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dxapp.json
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{
"name": "eggd_dias_batch",
"title": "eggd_dias_batch",
"version": "3.2.0",
"summary": "Launches downstream analyses for Dias",
"dxapi": "1.0.0",
"inputSpec": [
{
"name": "assay",
"label": "assay",
"class": "string",
"optional": true,
"help": "string of assay to run analysis for (CEN or TWE)",
"group": ""
},
{
"name": "assay_config_dir",
"label": "assay config dir",
"class": "string",
"optional": true,
"default": "project-Fkb6Gkj433GVVvj73J7x8KbV:/dynamic_files/dias_batch_configs/",
"help": "path to directory containing assay config files",
"group": ""
},
{
"name": "assay_config_file",
"label": "assay config file",
"class": "file",
"optional": true,
"help": "Config file for assay, if not provided will search assay_config_dir for files",
"group": ""
},
{
"name": "manifest_files",
"label": "manifest files",
"class": "array:file",
"optional": true,
"help": "manifest file(s) of sample -> panel",
"group": ""
},
{
"name": "qc_file",
"label": "QC file",
"class": "file",
"optional": true,
"help": "QC .xlsx file. optional input to eggd_artemis"
},
{
"name": "multiqc_report",
"label": "MultiQC report",
"class": "file",
"optional": true,
"help": "MultiQC report, optional input to eggd_artemis"
},
{
"name": "split_tests",
"label": "split tests",
"class": "boolean",
"default": true,
"help": "controls if to split multiple panels / genes in a manifest to individual reports instead of being combined into one"
},
{
"name": "exclude_samples",
"label": "exclude samples",
"class": "string",
"optional": true,
"help": "comma separated string of samples to exclude from CNV calling / CNV reports (these should be formatted as ` InstrumentID-SpecimenID` (i.e. `123245111-33202R00111`))"
},
{
"name": "exclude_samples_file",
"label": "exclude samples file",
"class": "file",
"optional": true,
"help": "file of samples to exclude from CNV calling / CNV reports, one sample name per line (`InstrumentID-SpecimenID` for Epic samples, X number for Gemini samples)"
},
{
"name": "exclude_controls",
"label": "exclude controls",
"class": "boolean",
"default": true,
"optional": true,
"help": "controls if to automatically exclude Epic control samples"
},
{
"name": "manifest_subset",
"label": "manifest subset",
"class": "string",
"optional": true,
"help": "comma separated string of samples in manifest on which to ONLY run jobs (these should be formatted as ` InstrumentID-SpecimenID` (i.e. `123245111-33202R00111`))"
},
{
"name": "single_output_dir",
"label": "single output directory",
"class": "string",
"optional": false,
"help": "path to output directory of dias single",
"group": ""
},
{
"name": "cnv_call_job_id",
"label": "CNV call job ID",
"class": "string",
"optional": true,
"help": "job ID of CNV calling to use for generating CNV reports, if running calling and reports together the job ID of the calling job will be used"
},
{
"name": "cnv_call",
"label": "cnv call",
"class": "boolean",
"optional": true,
"help": "run cnv calling",
"group": "mode"
},
{
"name": "cnv_reports",
"label": "cnv reports",
"class": "boolean",
"optional": true,
"help": "run cnv reports",
"group": "mode"
},
{
"name": "snv_reports",
"label": "snv reports",
"class": "boolean",
"optional": true,
"help": "run snv reports",
"group": "mode"
},
{
"name": "mosaic_reports",
"label": "mosaic reports",
"class": "boolean",
"optional": true,
"help": "run mosaic reports",
"group": "mode"
},
{
"name": "artemis",
"label": "artemis",
"class": "boolean",
"optional": true,
"help": "run eggd_artemis",
"group": "mode"
},
{
"name": "testing",
"label": "testing",
"class": "boolean",
"optional": true,
"help": "run in testing mode, will terminate all jobs",
"group": "test"
},
{
"name": "sample_limit",
"label": "sample limit",
"class": "int",
"optional": true,
"help": "no. of samples to limit launching reports workflow jobs for",
"group": "test"
},
{
"name": "unarchive",
"label": "unarchive",
"class": "boolean",
"optional": true,
"default": false,
"help": "controls whether to automatically unarchive any required files that are archived. Default is to fail the app with a list of files required to unarchive. If set to true, all required files will start to be unarchived and the job will exit with a zero exit code and the job tagged to state no jobs were launched"
},
{
"name": "unarchive_only",
"label": "unarchive_only",
"class": "boolean",
"optional": true,
"default": false,
"help": "controls if to only run the app to check for archived files and unarchive (i.e no launching of jobs), if all files are found in an unarchived state the app will exit with a zero exit code"
}
],
"outputSpec": [
{
"name": "summary_report",
"label": "summary report",
"class": "file",
"optional": true,
"help": "text file with summary of jobs launched and any errors encountered"
},
{
"name": "launched_jobs",
"label": "launched jobs",
"class": "string",
"optional": true,
"help": "comma separated string of launched jobs"
}
],
"runSpec": {
"timeoutPolicy": {
"*": {
"hours": 8
}
},
"interpreter": "python3",
"file": "resources/home/dnanexus/dias_batch/dias_batch.py",
"distribution": "Ubuntu",
"release": "20.04",
"version": "0",
"headJobOnDemand": true
},
"access": {
"network": [
"*"
],
"allProjects":"CONTRIBUTE",
"project": "CONTRIBUTE"
},
"developers":[
"org-emee_1"
],
"authorizedUsers": [
"org-emee_1"
],
"regionalOptions": {
"aws:eu-central-1": {
"systemRequirements": {
"*": {
"instanceType": "mem1_ssd1_v2_x2"
}
}
}
}
}