Inputs

Inputs can be provided in either CSV or YAML format.

For CSV inputs, identify the fields needed for each input type below and include the respective fields. For mixed inputs, use empty cell values - see template CSVs for examples.

For YAML inputs, see template YAMLs. In each template YAML, any key or value in <> needs to be filled in and the <> removed, ex. <patient1> should be filled in with the actual patient ID, e.g. PRAD0001. Other keys not in <> must be kept as they are.

---
input:
    <patient1>:
...

should be filled in to become:

---
input:
    PRAD0001:
...

Input BAM

Field	Type	Required	Description
patient	string	yes	Identifier for the patient
sample	string	yes	Identifier for the sample
state	string	yes	Must be either "tumor" or "normal"
path	path	yes	Absolute path to the sample BAM file

See this template for CSV format and this template for YAML format.

Input FASTQ

Field	Type	Required	Description
patient	string	yes	Identifier for the patient
sample	string	yes	Identifier for the sample
state	string	yes	Must be either "tumor" or "normal"
read_group_identifier	string	yes	Read group ID
sequencing_center	string	yes	Center where sequencing was performed
library_identifier	string	yes	Library used for sample
platform_technology	string	yes	Technology used for sequencing
platform_unit	string	yes	Name of specific platform unit
bam_header_sm	string	yes	Sample name tag for BAM
lane	string	yes	Lane identifier for sample
read1_fastq	path	yes	Absolute path to R1 FASTQ
read2_fastq	path	yes	Absolute path to R2 FASTQ

See this template for CSV format and this template for YAML format.

Input SRC

For SRC input, only call-SRC can be run. In this case, for each tumor sample, SNV calls and CNA calls must be provided.

Field	Type	Required	Description
patient	string	yes	Identifier for the patient
sample	string	yes	Identifier for the sample
state	string	yes	Must be either "tumor" or "normal"
src_input_type	string	yes	The type of input, must be either "CNA" or "SNV"
src_input_algorithm	string	yes	Algorithm used to generate the input
src_path	string	yes	Full path to the file

See this template for CSV format and this template for YAML format.

Mixed input

A mix of SRC and sequencing inputs can also be provided, in cases where for example CNA calling has already been done and SNV calling needs to be performed.

CNA calls available

If CNA calls are already available, provide the CNA calls as SRC input and provide the sequencing data (either FASTQ or BAM/CRAM) as FASTQ or BAM/CRAM input. With CSV input, keep all columns and leave fields black per row as needed. See template CSV for the CSV format and template YAML for the YAML format.

SNV calls available

If SNV calls are already available, provide the SNV calls as SRC input and provide the sequencing data (either FASTQ or BAM/CRAM) as FASTQ or BAM/CRAM input. With CSV input, keep all columns and leave fields black per row as needed. See template CSV for the CSV format and template YAML for the YAML format.

Input VCF

TO-DO

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