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# For this mapping, I followed the steps described in this tutorial: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-multi
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# download the human reference transcriptome
curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2020-A.tar.gz
tar -xf refdata-gex-GRCh38-2020-A.tar.gz

# download the pre-built V(D)J reference
curl -O https://cf.10xgenomics.com/supp/cell-vdj/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz
tar -xf refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz

# adjust the multiconfig file

# run the multi command in the multi map
nice -n 10 /scratch/etanis/software/cellranger-6.1.2/cellranger multi --id=dimitri --csv=/scratch/etanis/ST-118/multi/220510_multi-config-template_2.csv