validate sample sheet

Validates Illumina SampleSheets for use with bcl2fastq / bclconvert.

Currently validated fields include:

• Header
  • Check first line is [Header].
  • Check last line is [Data].
  • Check adapters contain only ATCG.
  • Check read(s) are valid integers.
  • Check investigator and experiment name set.

• Sample_ID
  • Check for presence of any non-alphanumeric characters, underscores or dashes.
  • Check for duplicates in sheet where lane OR index are not unique.
  • Check for missing sample ID.
  • (optional) use given regex patterns to validate sample ID against. Useful for where strict sample ID naming required that may break downstream analysis.

• Sample_Name
  • Check for presence of any non-alphanumeric characters, underscores or dashes.
  • Check for missing sample name.

Requirements

The following Python packages are required:

• pandas (>v1.0.0)

Usage

The only required input to be passed is the path to a sample sheet:

# sample sheet with no errors
$ python validate/validate.py --samplesheet Samplesheet.csv

Checking samplesheet for issues

SUCCESS: Samplesheet has passed validation.



# sample sheet with errors

$ python validate/validate.py --samplesheet SampleSheet.csv

Checking samplesheet for issues

Errors found in Sample_ID:

        Invalid characters in sample: 2106557 21211Z0021-BM-MPD-MYE-F-EGG2 in row 45
        Sample_ID in row 51 is missing / invalid: (nan)


Errors found in index:

        Invalid characters found in index: TGTTCCTAGAff at row 22

Regex patterns for checking sample IDs are valid against a required specification may be passed either as strings at the cmd line (--name_patterns pattern1 pattern2) or in a file (--name_patterns_file sample_patterns.txt).

n.b. if passing patterns at the cmd line these must be quoted to stop shell expansion.

$ python validate/validate.py --samplesheet SampleSheet.csv 
--name_patterns "[0-9]{7}-[A-Z0-9]*-[A-Za-z0-9-\(\)]*-MYE-[MF]-EGG2"

Errors found in index:

        Invalid characters found in index: TGTTCCTAGAff at row 22


Errors found in Sample_ID:

        Invalid characters in sample: 2106557 21211Z0021-BM-MPD-MYE-F-EGG2 in row 45
        Sample_ID in row 51 is missing / invalid: (nan)
        Sample ID 2106557 21211Z0021-BM-MPD-MYE-F-EGG2 is invalid, please ensure it conforms to the expected format for the given sample assay
        Sample ID 2106298_20-21202Z0083_20-PB-MPD-MYE-M-EGG2 is invalid, please ensure it conforms to the expected format for the given sample assay
        Sample ID 2106298_PH-21202Z0083_PH-PB-MPD-MYE-M-EGG2 is invalid, please ensure it conforms to the expected format for the given sample assay