Input JSON for hic.wdlΒΆ

Optional parameters and flags are marked with ?.

  1. Reference genome

    Currently supported genomes:

  2. Input genome data files

    Choose any genome data type you want to start with and do not define others.

    • "hic.fastq"? : 3-dimensional array with FASTQ file path/URI. Next step is to be aligned and converted to bams.
      • 1st dimension: read number ID
      • 2nd dimension: sequencing run ID
      • 3rd dimension: library ID
    • "hic.bams"? : 3-dimensional array of raw (unfiltered) BAM file path/URI. Next step is to be merged.
      • 1st dimension: specific bam types ID
      • 2nd dimension: grouping of collisions, collisions_low_mapq, unmapped, mapq0, alignable
      • 3rd dimension: library ID
    • "hic.input_sort_files"? : 2-dimensional array of not merged sort.txt files. Next step is to be merged.
      • 1st dimension: sequencing run ID
      • 2nd dimensions: library ID
    • "hic.input_merged_sort"? : 1-dimensional array of merged sort.txt files. Next step is to be deduped.
      • 1st dimension: library ID
    • "hic.input_dedup_pairs"? : 1-dimensional array of read pairs with no duplicates. Next step is to be merged.
      • 1st dimension: library ID
    • "hic.input_pairs"? : Single file of merged read pairs with no duplicates. Next step is to create a .hic file.
    • "hic.chrsz"? : Single chrom.sizes file. Used for alignment and creation of .hic file.
    • "hic.restriction_sites"? : Single file containing locations of restriction sites in genome. Used for alignment.
    • "hic.reference_index"? : Single reference sequence file. Used for alignment.

    "hic.restriction_sites" and "hic.reference_index" must only be defined if starting from fastq files.