@include "rna/_cr_lib_stages.mro"

call WRITE_POS_BAM(
    bam_header        = "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/join-ufe8a67f765/files/bam_header",
    alignments        = [
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk00-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk01-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk02-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk03-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk04-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk05-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk06-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk07-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk08-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk09-ufe8a67f766/files/pos_sorted.asf",
        "/gpfs/data/yanailab/public/linda_share/maayan_STalign/ST358_A1/SPATIAL_RNA_COUNTER_CS/SPATIAL_RNA_COUNTER/_BASIC_SPATIAL_RNA_COUNTER/_MATRIX_COMPUTER/ALIGN_AND_COUNT/fork0/chnk10-ufe8a67f766/files/pos_sorted.asf",
    ],
    read_chunks       = [
        {
            "chemistry": {
                "barcode_read_length": 16,
                "barcode_read_offset": 0,
                "barcode_read_type": "R1",
                "barcode_whitelist": "visium-v1",
                "description": "Spatial 3' v1",
                "endedness": "three_prime",
                "name": "SPATIAL3Pv1",
                "read_type_to_bcl2fastq_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "R1",
                    "R2": "R2",
                },
                "read_type_to_bcl_processor_filename": {
                    "I1": "I1",
                    "I2": null,
                    "R1": "RA",
                    "R2": null,
                },
                "rna_read2_length": null,
                "rna_read2_offset": 0,
                "rna_read2_type": null,
                "rna_read_length": null,
                "rna_read_offset": 0,
                "rna_read_type": "R2",
                "si_read_length": null,
                "si_read_offset": 0,
                "si_read_type": "I1",
                "strandedness": "+",
                "umi_min_read_length": 10,
                "umi_read_length": 12,
                "umi_read_offset": 16,
                "umi_read_type": "R1",
            },
            "chunk_id": 0,
            "fastqs": {
                "i1": null,
                "i2": null,
                "r1": "/gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/BS20957A_S1_R1_001.fastq.gz",
                "r1_interleaved": false,
                "r2": "/gpfs/data/yanailab/projects/lp2700/data_raw/Project_Yanai_FCH3HY3BGXT_2023Apr05_fastq/Sample_BS20957A/BS20957A_S1_R2_001.fastq.gz",
            },
            "gem_group": 1,
            "library_id": 0,
            "library_type": "Gene Expression",
            "read_group": "ST358_A1:0:1:H3HY3BGXT:1",
            "read_lengths": {},
            "subsample_rate": null,
        },
    ],
    target_set_name   = null,
    barcode_to_sample = null,
)
