example_inputs.yaml

{
    "R1_output_fastq": "processed_fastq_R1.fastq.gz",
    "R2_output_fastq": "processed_fastq_R2.fastq.gz",
    "abra2_bam_index": true,
    "abra2_consensus_sequence": null,
    "abra2_contig_anchor": null,
    "abra2_maximum_average_depth": null,
    "abra2_maximum_mixmatch_rate": null,
    "abra2_no_edge_complex_indel": true,
    "abra2_no_sort": true,
    "abra2_output_bams": "test_abra.bam",
    "abra2_scoring_gap_alignments": null,
    "abra2_soft_clip_contig": null,
    "abra2_window_size": null,
    "bedtools_genomecov_option_bedgraph": true,
    "bedtools_merge_distance_between_features": null,
    "bwa_mem_K": 1000000,
    "bwa_mem_M": null,
    "bwa_mem_P": null,
    "bwa_mem_T": 30,
    "bwa_mem_Y": true,
    "bwa_mem_output": "test_alignment.sam",
    "bwa_number_of_threads": null,
    "comment": null,
    "create_bam_index": true,
    "description": null,
    "duplicate_scoring_strategy": null,
    "fastp_failed_reads_output_file_name": null,
    "fastp_html_output_file_name": "test_fastp_out.html",
    "fastp_json_output_file_name": "test_fastp_out.json",
    "fastp_minimum_read_length": 25,
    "fastp_read1_adapter_sequence": "GATCGGAAGAGC",
    "fastp_read1_output_file_name": "trimmed_fastp_R1.fastq.gz",
    "fastp_read2_adapter_sequence": "AGATCGGAAGAGC",
    "fastp_read2_output_file_name": "trimmed_fastp_R2.fastq.gz",
    "fastp_unpaired1_output_file_name": null,
    "fastp_unpaired2_output_file_name": null,
    "fgbio_fastq_to_bam_input": [
[
        {
            "class": "File",
            "path": "/path/to/Sample_R1_part1.fastq.gz"
        },
        {
            "class": "File",
            "path": "/path/to/Sample_R2_part1.fastq.gz"
        }
],
[
        {
            "class": "File",
            "path": "/path/to/Sample_R1_part2.fastq.gz"
        },
        {
            "class": "File",
            "path": "/path/to/Sample_R2_part2.fastq.gz"
        }
]
    ],
    "fgbio_fastq_to_bam_output_file_name": null,
    "fgbio_fastq_to_bam_predicted-insert-size": null,
    "fgbio_fastq_to_bam_sort": null,
    "fgbio_fastq_to_bam_umi-tag": null,
    "gatk_mark_duplicates_assume_sort_order": null,
    "gatk_mark_duplicates_duplication_metrics_file_name": "test_dup_metrics.txt",
    "gatk_mark_duplicates_output_file_name": null,
    "gatk_merge_bam_alignment_output_file_name": null,
    "gatk_merge_sam_files_output_file_name": "test_unmapped.sam",
    "gatk_sam_to_fastq_include_non_pf_reads": null,
    "gatk_sam_to_fastq_include_non_primary_alignments": null,
    "library": "test",
    "merge_sam_files_sort_order": "queryname",
    "optical_duplicate_pixel_distance": 1500,
    "picard_addRG_sort_order": "queryname",
    "picard_addRG_output_file_name": "test_addRG.bam",
    "picard_fixmateinformation_output_file_name": "test_fx.bam",
    "platform": "ILLUMINA",
    "platform-model": "novaseq",
    "platform-unit": "IDT11",
    "read-group-id": "test",
    "read-structures": [
        "3M2S+T",
        "3M2S+T"
    ],
    "read_name_regex": null,
    "reference_sequence": {
        "class": "File",
        "metadata": {},
        "path": "/path/to/reference.fasta",
        "secondaryFiles": []
    },
    "run-date": null,
    "sample": "test",
    "sequencing-center": "MSKCC",
    "sort_order": "coordinate",
    "unpaired_fastq_file": null,
    "validation_stringency": "LENIENT"
}