@include "_common_stages.mro"

call EXTRACT_READS(
    chunks = [
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0000.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0000.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0001.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0001.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0002.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0002.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0003.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0003.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0004.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0004.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0005.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0005.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0006.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0006.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0007.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0007.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0008.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0008.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0009.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0009.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
                "endedness": "three_prime",
                "name": "SC3Pv3",
                "umi_read_length": 12,
                "si_read_length": null,
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2"
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": "I2",
                    "R1": "RA",
                    "R2": null
                }
            },
            "read_chunks": {
                "R1": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R1-0010.fastq.lz4",
                "R2": "/ufrc/ewang/lancetdenes/libLTD/h2b_run2/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/CHUNK_READS/fork0/chnk0-u85e8936f7c/files/R2-0010.fastq.lz4"
            }
        },
        {
            "gem_group": 1,
            "library_type": "Gene Expression",
            "read_group": "h2b_run2:0:1:HJ5NCBGXB:1",
            "subsample_rate": 1.0,
            "library_id": "0",
            "reads_interleaved": false,
            "chemistry": {
                "si_read_offset": 0,
                "strandedness": "+",
                "umi_read_offset": 16,
                "barcode_read_type": "R1",
                "umi_read_type": "R1",
                "barcode_read_length": 16,
                "rna_read_type": "R2",
                "barcode_whitelist": "3M-february-2018",
                "si_read_type": "I1",
                "rna_read_length": null,
                "description": "Single Cell 3' v3",
                "rna_read_offset": 0,
                "barcode_read_offset": 0,
                "rna_read2_type": null,
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    initial_reads = null,
    primers = [
        {
            "name": "P5",
            "seq": "AATGATACGGCGACCACCGAGATCT"
        },
        {
            "name": "P7",
            "seq": "CAAGCAGAAGACGGCATACGAGAT"
        },
        {
            "name": "R1",
            "seq": "ACACTCTTTCCCTACACGACG"
        },
        {
            "name": "R2",
            "seq": "GTGACTGGAGTTCAGACGTGTG"
        },
        {
            "name": "switch_oligo",
            "seq": "AAGCAGTGGTATCAACGCAGAGTACATGGG"
        },
        {
            "name": "polyA",
            "seq": "AAAAAAAAAAAAAAAAAAAA"
        }
    ],
    align = {
        "aligner": "star",
        "high_conf_mapq": null
    },
    r1_length = null,
    r2_length = null,
    skip_metrics = false,
    reference_path = "/ufrc/ewang/lancetdenes/refdata-cellranger-mm10-3.0.0",
    feature_reference = null,
    augment_fastq = false,
    library_info = [
        {
            "gem_group": 1,
            "library_id": "0",
            "library_type": "Gene Expression"
        }
    ],
)