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Loading Scout cases

When loading a case into scout it is possible to use either a config file or to specify parameters on the command line. The most common way to load a case is to use a config file, which is a .yaml file that contains all information describing the case and its samples. The command to load a case with a config file is: scout load case my_config.yaml

Scout Load Config

The loading config is a .yaml file and can include all the necessary information to scout. Command line options will overload information in the config file. For a complete spec of the config file see load config

An example file, (this file is located in scout/demo/643594.config.yaml):

---

owner: cust000

family: '643594'
samples:
  - analysis_type: wes
    sample_id: ADM1059A2
    capture_kit: Agilent_SureSelectCRE.V1
    father: ADM1059A1
    mother: ADM1059A3
    sample_name: NA12882
    phenotype: affected
    sex: male
    bam_path: path/to/bam
  - analysis_type: wes
    sample_id: ADM1059A1
    capture_kit: Agilent_SureSelectCRE.V1
    father: '0'
    mother: '0'
    sample_name: NA12877
    phenotype: unaffected
    sex: male
    bam_path: path/to/bam
  - analysis_type: wes
    sample_id: ADM1059A3
    capture_kit: Agilent_SureSelectCRE.V1
    father: '0'
    mother: '0'
    sample_name: NA12878
    phenotype: unaffected
    sex: female
    bam_path: path/to/bam

vcf_snv: scout/demo/643594.clinical.vcf.gz
vcf_sv: scout/demo/643594.clinical.SV.vcf.gz
vcf_snv_research: scout/demo/643594.research.vcf.gz
vcf_sv_research: scout/demo/643594.research.SV.vcf.gz

madeline: scout/demo/madeline.xml
default_gene_panels: [panel1]
gene_panels: [panel1]

# metadata
rank_model_version: '1.12'
sv_rank_model_version: '1.5'
rank_score_threshold: -100
analysis_date: 2016-10-12 14:00:46
human_genome_build: '37'

Adding custom reports to the case

A number of case-associated reports (supported formats: HTML, PDF, Excel) can be loaded and displayed/downloaded on the case sidebar page:

image

While case General report and mtDNA report (the latter only available for non-cancer cases) are generated the moment a user clicks on their link, other types of reports are pre-existing documents that can be associated with the case immediately when it is loaded in Scout (by adding them to the case load config file) or later, using the command line.

Available types or case reports: - cnv: Copy Number Variants Report (PDF), available only for cancer cases - cov_qc: Coverage QC Report (HTML), available only for cancer cases - delivery: Delivery Report (HTML) - exe_ver: Pipeline detailed software versions (YAML) - gene_fusion: A report (PDF) showing gene fusions from RNA-Seq data, analysis limited to the clinical gene list - gene_fusion_research: A report (PDF) showing gene fusions from RNA-Seq data, performed on all genes - multiqc: MultiQC Report (HTML) - multiqc_rna: MultiQC RNA report (HTML) - reference_info: Pipeline detailed reference file versions (YAML) - RNAfusion_inspector: nf-core rnafusion RNA Fusion Inspector file (HTML) - RNAfusion_inspector_research: nf-core rnafusion research RNA Fusion Inspector file (HTML) - RNAfusion_report: nf-core rnafusion RNA fusion report file (HTML) - RNAfusion_report_research: nf-core rnafusion research RNA fusion report file (HTML)

All these reports reflect the items present in this dictionary

Use the following command to load/update a report for a pre-existing case:

scout load report -t <report-type>

Usage: scout load report [OPTIONS] CASE_ID REPORT_PATH

  Load a report document for a case.

Options:
  -t, --report-type [delivery|cnv|cov_qc|exe_ver|multiqc|multiqc_rna|gene_fusion|gene_fusion_research|reference_info|RNAfusion_inspector|RNAfusion_inspector_research|RNAfusion_report|RNAfusion_report_research|saltshaker_report]
                                  Type of report  [required]

Adding custom images to a case

Scout can display custom images as new panels on the case view or variant view which could be used to display analysis results from a separate pipeline. The custom images are defined in the case config file. Scout stores image metadata (for example title, description, dimensions and path) in the database, while image files are read from disk when rendered. Scout currently supports gif, jpeg, png and svg images.

The syntax for loading an image differs depending on where it is going to be displayed. Images on the case view can be grouped into different groups that are displayed as accordion-type UI elements named after the group. Images can be associated with structural variants with a given HGNC symbol.

The fields title, description and path are mandatory regardless of location. The image size can be defined with the optional parameters width and height. The image height and width unit is pixels.


custom_images:
  case_images:
    group_one:
      - title: <string> title of image [mandatory]
        description: <string> replacement description of image [mandatory]
        width: <int> 500
        height: <int> 100
        path: <string> scout/demo/images/custom_images/640x480_one.png [mandatory]
      - title: <string> A jpg image [mandatory]
        description: <string> A very good description [mandatory]
        width: <string> 500
        path: <string> scout/demo/images/custom_images/640x480_two.jpg [mandatory]
    group_two:
      - title: <string> An SVG image [mandatory]
        description: <string> Another very good description
        path: <string> scout/demo/images/custom_images/640x480_three.svg [mandatory]
  str_variants_images:
    - title: <string> title of image [mandatory]
      str_repid: AFF2 [mandatory]
      description: <string> replacement description of image [mandatory]
      width: <string> 500
      height: <string> 100
      path: <string> scout/demo/images/custom_images/640x480_one.png [mandatory]
    - title: <string> A jpg image [mandatory]
      str_repid: AFF2 [mandatory]
      description: <string> A very good description [mandatory]
      width: <string> 500
      path: <string> scout/demo/images/custom_images/640x480_two.jpg [mandatory]
Loading multiple images with wildcards

If you have multiple images you would like to associate with different variants, you can use wildcards to reduce the number of lines in the load config file. For example, you have two images 640x480_AR.svg and 640x480_ATN1.svg that should be attached to variants in AR and ATN1. Instead of writing a long list with one entry per image, you can use wildcards to flag which part of the path name corresponds to the REPID. Wildcards are a variable name surrounded by curly brackets, {VARIABLE_NAME}. The variable name can contain letters, numbers and underscores.

When custom image metadata is loaded the algorithm finds files matching the pattern and substitutes the wildcard with the string. In other words this expands the path using the configuration pattern and populates the case object accordingly.

Given the two files above, this configuration

custom_images:
  str_variants_images:
    - title: <string> A jpg image {REPID} [mandatory]
      str_repid: {REPID} [mandatory]
      path: <string> scout/demo/images/custom_images/640x480_{REPID}.jpg [mandatory]

is equivalent to

custom_images:
  str_variants_images:
    - title: <string> An image of AR
      str_repid: AR
      path: <string> scout/demo/images/custom_images/640x480_AR.jpg
    - title: <string> An image of ATN1
      str_repid: ATN1
      path: <string> scout/demo/images/custom_images/640x480_ATN1.jpg

Load case from CLI without config

Cases can be loaded without config file, in that case the user needs to specify a ped file and optionally one or several VCF files. An example could look like

scout load case --ped path/to/file.ped --vcf-snv path/to/file.vcf

Please use

scout load case --help

for more instructions