search

epam / fonda

Fonda is a framework which offers scalable and automatic analysis of multiple NGS sequencing data types
Apache License 2.0
8 stars 2 forks source link

Feature Library duplicate samples #169

Closed syansanofi closed 4 years ago

syansanofi commented 4 years ago

In the SCRnaExpressionCellRangerFastq workflow, there are certain situations where multiplexed adt libraries (Antibody, Custom, CRISPR) can be used with individual gene expression samples. This creates a situation where single ADT will need to be used with multiplex GEX samples. This is not allowed currently and produces following error

[main] ERROR com.epam.fonda.Main - Error step in main: java.lang.IllegalArgumentException: Multiple sample types or matched controls in a sample
An example of the sample manifest is below: parameterType shortName libtype master
fastqFile mRNA1 GEX mRNA1
fastqFile mRNA2 GEX mRNA2
fastqFile ADT_HTO custom mRNA1
fastqFile ADT_HTO custom mRNA2
kamyshova commented 4 years ago

@syansanofi Hi, Shu. I've created the draft pull request with the solution. One question is should we rely on the fact that the ADT will contain 'ADT' (case-insensitive) in its name? Or are other options possible? Alternatively, we can skip this check entirely for the SCRnaExpressionCellRangerFastq workflow.

syansanofi commented 4 years ago

@kamyshova Yes we can remove it. The ADT is just a string placeholder that I used. The libraries naming does not have any restrictions normally.

kamyshova commented 4 years ago

@syansanofi the PR was updated. Could you check this?

kamyshova commented 4 years ago

@syansanofi The related PR #170 is in the develop branch. Could we close the issue?

syansanofi commented 4 years ago

Yes, closing issue. Thank you!