Quantms. validator issue

[anoushkabhat13]

Description of the bug

Description

The SDRF validator rejects pooled as a value for
characteristics[biological replicate] by requiring the column to contain
positive integers only.

However, the SDRF documentation states that for pooled samples, pooled
should be used for individual-specific fields such as biological replicate,
age, and sex.

As a result, valid SDRF files for TMT reference channels fail validation.

Expected behavior

For pooled samples, the following should be accepted:

characteristics[pooled sample] = pooled
or
characteristics[pooled sample] = SN=sample1;SN=sample2

and

characteristics[biological replicate] = pooled

Similarly, pooled should also be accepted in other individual-specific
fields (e.g. age, sex) if this is the intended SDRF convention.

Actual behavior

Validation fails with:

cat <<-END_VERSIONS > versions.yml
"BIGBIO_QUANTMS:QUANTMS:INPUT_CHECK:SAMPLESHEET_CHECK":
quantms-utils: $(pip show quantms-utils | grep "Version" | awk -F ': ' '{print $2}')
END_VERSIONS

Command exit status:
1

Command output:
Non-integer values found in the following columns and rows: {'characteristics[biological replicate]':....

Command used and terminal output

Relevant files

No response

System information

Environment

• quantms pipeline: 1.6.0
• quantms-utils: 0.0.23 (Docker image)
• Nextflow: 24.10.5
• running on EC2 Instance in AWS