scrna demultiplexing workflow

Quickstart

1. Download test dataset

wget https://mondriantestdata.s3.amazonaws.com/10x_test_data.tar.gz
tar -xvf 10x_test_data.tar.gz

2. Download reference datasets.

wget https://mondriantestdata.s3.amazonaws.com/reference_grch38_scrna.tar.gz
tar -xvf reference_grch38_scrna.tar.gz

3. Launch pipeline

nextflow run shahcompbio/scrna_demultiplexing \
  -profile singularity \
  --output_dir outputs \
  --jobmode local \
  --numcores 16 \
  --meta_yaml $PWD/10x_test_data/meta.yaml \
  --gex_fastq $PWD/10x_test_data/gex  \
  --gex_id PBMC-ALL_60k_universal_HashAB1-4_BL_4tags_Rep1_gex \
  --cite_fastq $PWD/10x_test_data/cite \
  --cite_id PBMC-ALL_60k_universal_HashAB1-4_BL_4tags_Rep1_ab \
  --reference $PWD/reference_grch38_scrna/GRCh38/ \
  --vdj_reference $PWD/reference_grch38_scrna/refdata-cellranger-vdj-GRCh38-alts-ensembl-7.1.0 \
  --sample_id SAMP123 \
  --bcr_fastq $PWD/10x_test_data/cite \
  --bcr_id PBMC-ALL_60k_universal_HashAB1-4_BL_4tags_Rep1_ab

Workflow use cases

Gene Expression	Cite Seq	HTO	VDJ-B	VDJ-T	Steps	Testing
✔️	✖️	✖️	✖️	✖️	NonMultiplex	✔️
✔️	✖️	✔️	✖️	✖️	DeMultiplex	✔️
✔️	✔️	✖️	✖️	✖️	NonMultiplex	✔️
✔️	✔️	✖️	✔️	✖️	NonMultiplex	✔️
✔️	✔️	✖️	✖️	✔️	NonMultiplex	✔️
✔️	✔️	✖️	✔️	✔️	NonMultiplex	✔️
✔️	✔️	✔️	✖️	✖️	DeMultiplex	✔️
✔️	✖️	✔️	✔️	✖️	DeMultiplex	✔️
✔️	✖️	✔️	✖️	✔️	DeMultiplex	✔️
✔️	✖️	✔️	✔️	✔️	DeMultiplex	✔️
✔️	✔️	✔️	✔️	✖️	DeMultiplex	✔️
✔️	✔️	✔️	✖️	✔️	DeMultiplex	✔️
✔️	✔️	✔️	✔️	✔️	DeMultiplex	✔️

Logic can be summed up with this pseudocode

if HTO:
    CELLRANGERMULTI(gex_fastq, cite_fastq)   -> {raw_h5, [['sample': filtered_h5, bam], ...]}
    for sample in CELLRANGERMULTI:
      BAM2FASTQ(sample.bam)
      CELLRANGERMULTI(bam2fastq.gex_fastq, cite_fastq,vdj_b_fastq, vdj_t_fastq) -> {raw_h5, ['sample': filtered_h5, bam]}
      CELLBENDER(CELLRANGERMULTI.raw_h5)
else:
    CELLRANGERMULTI(gex_fastq, cite_fastq,vdj_b_fastq, vdj_t_fastq) -> {raw_h5, ['sample': filtered_h5, bam]}
    CELLBENDER(CELLRANGERMULTI.raw_h5)