scRnaExpression Fastq does not invoke QC (hangs cohort analysis)

[syansanofi]

Running scRnaExpression Fastq with toolset=count+vdj+qc hangs because individual sample shell scripts do not have QC portion. Another effect is that qc metrics in Result_summary directory is not written.

Example sample script portion

echo `date` Begin Step: Generate gene-barcode matrix...
/site/ne/home/wings/bfx_tools/cellranger/v3.1.0/cellranger-cs/3.1.0/bin/cellranger mat2csv /common/analysis/count/2-25-2020_PBMC_with_HTO_and_ADT-1/outs/filtered_feature_bc_matrix 2-25-2020_PBMC_with_HTO_and_ADT-1_GRCh38_umi_count_matrix.csv
tr '\,' '\t' < 2-25-2020_PBMC_with_HTO_and_ADT-1_GRCh38_umi_count_matrix.csv > 2-25-2020_PBMC_with_HTO_and_ADT-1_GRCh38_umi_count_matrix.tsv
rm 2-25-2020_PBMC_with_HTO_and_ADT-1_GRCh38_umi_count_matrix.csv

if [ $? -eq 0 ]
then
    echo `date` Successful Step: Generate gene-barcode matrix.
    sleep 8
else
    echo `date` Error Step: Generate gene-barcode matrix.

    echo `date` The job was aborted due to ERRORS found.
    exit 1;
fi

echo `date` Begin Step: Merge gene-barcode matrix...

echo `date` Begin Step: Remove temporary directories...

if [ $? -eq 0 ]
then
    echo `date` Successful Step: Remove temporary directories.
    sleep 8
else
    echo `date` Error Step: Remove temporary directories.

    echo `date` The job was aborted due to ERRORS found.
    exit 1;
fi
echo `date` Finish the job execution!

[syansanofi]

Added further steps to sanitize non GEX samples. @kamyshova TY

[kamyshova]

@syansanofi Hi Shu, Thank you! Can we merge request #176 to develop? If it's ok, can you approve the request, please?

[syansanofi]

Yes please! TY