Create multiple cases using sample sheet file

By selecting "Create multiple cases", a batch of cases can be created using a tsv format sample sheet file. 

After selecting Create multiple cases, user enters a page where a sample sheet can be uploaded. The sample sheet is a tab separated text file (TSV file) defining all the necessary information for secondary and tertiary analysis launching for the batch of cases to be created.

The sample sheet should follow the format described below. Download a template file here: download sample

Sample sheet format

Columns are expected in the following order: 

1. case_id - required 
   1. Description: Case identifier in Nostos systems
   2. Valid input: non-empty string 
2. sample_id_proband - required 
   1. Description: Sample identifier of the fastq files (R1,R2) for the proband. We assume exactly 2 files in the input folder start with this sample id, and support currently no automatic merging of data split per lanes. We assume orientation of the read is specified in the file name after the sample id as "R1", "R2", according to Illumina naming convention. Example: FASTQ file names: NS012345_S1_L001_R1_001.fastq.gz, NS012345_S1_L001_R2_001.fastq.gz, sample id to use: NS012345
   2. Valid inputs: non-empty string 
3. sample_id_mother - required for trio analysis
   1. Description: Sample identifier of the fastq files (R1,R2) for the mother
   2. Valid inputs: non-empty string 
4. sample_id_father - required for trio analysis  
   1. Description: Sample identifier of the fastq files (R1,R2) for the mother.  Notice! Analysis with only one parent is currently not supported, so sample_id_mother is required if sample_id_father is defined, and vice versa.
   2. Valid input: non-empty string
5. sample_type  - required -
   1. Description: The sample type defining the sequencing method of the samples (whole genome sequencing (WGS), whole exome sequencing (WES), gene panel (GP)) 
   2. Valid input options: WES/WGS/GP 
6. bed_file  -  required for sample type WES and GP  
   1. Description:  Filename of a BED file defining the target region of the sequencgin/kit used. The BED file needs to be preuploaded. contact Nostos support for this onboarding step. Required when sample type WES or GP, not applicable to sample type WGS.
   2. Valid input: Filename of a BED file that is preuploaded in AWS s3
7. genetic_sex - required
   1. Description: The genetic sex of the patient
   2.  Valid input options: male/female
8. ref_genome - required
   1. Description: The version of human reference genome to be used in the analysis
   2. Valid input options: hg19/hg38 
9. date_of_birth - optional
   1. Description: Date of birth of the proband
   2. Valid input:  A single date in ISO format (e.g. 2010-10-13) or slash-separated DMY (e.g. 13/10/2010)
10. hpo_ids - optional
    1. Description: Patient symptoms/phenotype description in Human Phenotype Oncology (HPO) terms
    2. Valid input: List of HPO ids under Phenotypic abnormality, as root of the phenotypic abnormality subontology of the HPO. (e.g. HP:0000002) separated by comma (,), space (  ) or semicolon (;) 
11. affected_status_mother - required for trio 
12. affected_status_father - required for trio
    1. Description: Status of affectedness of the father with the same symptoms as patient. 
    2. Valid input options: affected/unaffected