Running 4DN pipelines using Tibanna

  • For 4DN pipelines, benchmark functions are pre-implemented in Tibanna through the Benchmark package. This means that the user does not have to choose EC2 instance type or EBS size (they are auto-determined). However, if the user wants to specify them, the following fields can be used. EBS_optimized makes IO slightly faster, but it is not supported by all isntance types. If you’re not sure, choose false.

Example

"config": {
  "instance_type": "instance_type",
  "ebs_size": 10,
  "EBS_optimized": false,

General Quality Control

md5

md5_4dn_run

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
  "args": {
    "app_name": "md5",
    "app_version": "0.2.6",
    "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/pipelines-cwl/0.2.6/cwl_awsem_v1/",
    "cwl_version": "v1",
    "cwl_main_filename": "md5.cwl",
    "input_files": {
      "input_file": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_INPUT_FILE_NAME_IN_INPUT_BUCKET>"
      }
    },
    "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
    "output_target": {
      "report": "<YOUR_OUTPUT_FILE_NAME_IN_OUTPUT_BUCKET>"
    }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}

fastqc

fastqc_4dn_run

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
    "args" {
      "app_name": "fastqc-0-11-4-1",
      "app_version": "0.2.0",
      "cwl_version": "v1",
      "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/pipelines-cwl/0.2.6/cwl_awsem_v1/",
      "cwl_main_filename": "fastqc-0-11-4-1.cwl",
      "cwl_child_filenames": ["fastqc-0-11-4.cwl"],
      "input_files": {
          "input_fastq": {
             "bucket_name": "<YOUR_INPUT_BUCKET>",
             "object_key": "<YOUR_INPUT_FILE>"
          }
      },
      "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
      "output_target": {
          "report_zip": "<YOUR_OUTPUT_REPORT_NAME>.zip"
      }
    },
    "config": {
      "log_bucket" : "<YOUR_LOG_BUCKET>",
      "key_name": "<YOUR_KEY_NAME>"
    }
}

Hi-C data processing & QC

  • Example full pipeline run

hic_4dn_run

bwa-mem

bwa_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
  "args": {
    "app_name": "bwa-mem",
    "app_version": "0.2.6",
    "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/pipelines-cwl/0.2.6/cwl_awsem_v1/",
    "cwl_main_filename": "bwa-mem.cwl",
    "cwl_version": "v1",
    "input_files": {
      "fastq1": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_FASTQ_FILE_R1>"
      },
      "fastq2": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_FASTQ_FILE_R2>"
      },
      "bwa_index": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_TGZ_BWA_INDEX_FILE>"
      }
    },
    "input_parameters": {
        "nThreads": 2
    },
    "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
    "output_target": {
      "out_bam": "<YOUR_OUTPUT_BAM_FILE>.bam"
    }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}

hi-c-processing-bam

hicbam_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
  "args": {
    "app_name": "hi-c-processing-bam",
    "app_version": "0.2.6",
    "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/pipelines-cwl/0.2.6/cwl_awsem_v1/",
    "cwl_main_filename": "hi-c-processing-bam.cwl",
    "cwl_child_filenames": [
      "pairsam-parse-sort.cwl",
      "pairsam-merge.cwl",
      "pairsam-markasdup.cwl",
      "pairsam-filter.cwl",
      "addfragtopairs.cwl"
    ],
    "input_files": {
      "chromsize": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_INPUT_CHROMSIZES_FILE>"
      },
      "input_bams": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": [
          "<YOUR_BAM_FILE1>",
          "<YOUT_BAM_FILE2>",
          "<YOUT_BAM_FILE3>"
        ]
      },
      "restriction_file": {
         "bucket_name": "<YOUR_INPUT_BUCKET>",
         "object_key": "<YOUR_RESTRICTION_SITE_FILE>"
      }
    },
    "input_parameters": {
      "nthreads_parse_sort": 8,
      "nthreads_merge": 8
    },
    "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
    "output_target": {
      "out_pairs": "<YOUR_OUTPUT_PAIRS_FILE>.pairs.gz",
      "merged_annotated_bam": "<YOUR_OUTPUT_MERGED_BAM_FILE>.bam"
    },
    "secondary_output_target": {
      "out_pairs": "<YOUR_OUTPUT_PAIRS_FILE>.pairs.gz.px2"
    }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}

hi-c-processing-pairs

hicpairs_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
  "args": {
    "app_name": "hi-c-processing-pairs",
    "app_version": "0.2.6",
    "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/pipelines-cwl/0.2.6/cwl_awsem_v1/",
    "cwl_main_filename": "hi-c-processing-pairs.cwl",
    "cwl_child_filenames": [
      "merge-pairs.cwl",
      "addfragtopairs.cwl",
      "pairs2hic.cwl",
      "cooler.cwl",
      "cool2mcool.cwl",
      "extract-mcool-normvector-for-juicebox.cwl",
      "add-hic-normvector-to-mcool.cwl"
    ],
    "cwl_version": "v1",
    "input_files": {
      "chromsizes": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_INPUT_CHROMSIZES_FILE>"
      },
      "input_pairs": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": [
            "<YOUR_INPUT_PAIRS_FILE1>",
            "<YOUR_INPUT_PAIRS_FILE2>",
            "<YOUR_INPUT_PAIRS_FILE3>"
        ]
      },
      "restriction_file": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_RESTRICTION_SITE_FILE>"
      }
    },
    "input_parameters": {
      "ncores": 1,
      "maxmem": "8g"
    },
    "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
    "output_target": {
      "mcool": "<YOUR_OUTPUT_MULTIRES_COOL_FILE>.mcool",
      "merged_pairs": "<YOUR_OUTPUT_MERGED_PAIRS_FILE>.pairs.gz",
      "hic": "<YOUR_OUTPUT_HIC_FILE>.hic"
    },
    "secondary_output_target": {
      "output_pairs": "<YOUR_OUTPUT_MERGED_PAIRS_FILE>.pairs.gz.px2"
    }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}

pairsqc

pairsqc_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
    "args": {
      "app_name": "pairsqc-single",
      "app_version": "0.2.6",
      "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/pipelines-cwl/0.2.6/cwl_awsem_v1/",
      "cwl_main_filename": "pairsqc-single.cwl",
      "cwl_version": "v1",
      "input_files": {
        "input_pairs" : {
          "bucket_name": "<YOUR_INPUT_BUCKET>",
          "object_key": "<YOUR_PAIRS_FILE>"
        },
        "chromsizes" : {
          "bucket_name": "<YOUR_INPUT_BUCKET>",
          "object_key": "<YOUR_INPUT_CHROMSIZES_FILE>"
        }
      },
      "secondary_files": {
        "input_pairs": {
          "bucket_name": "<YOUR_INPUT_BUCKET>",
          "object_key": "<YOUR_PAIRS_FILE>.px2"
        }
      },
      "input_parameters" :  {
        "enzyme": "6",
        "sample_name": "4DNFI1ZLO9D7",
        "max_distance": 8.2
      },
      "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
      "output_target": {
        "report": "<YOUR_OUTPUT_REPORT_FILE>.zip"
      }
    },
    "config": {
      "log_bucket": "<YOUR_LOG_BUCKET>",
      "key_name": "<YOUR_KEY_NAME>"
    }
}

Repli-seq data processing & QC

repliseq-parta

repliseq_a_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
  "args": {
    "app_name": "repliseq-parta",
    "app_version": "v14",
    "cwl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/docker-4dn-repliseq/v14/cwl/"
    "cwl_main_filename": "repliseq-parta.cwl",
    "cwl_child_filenames": ["clip.cwl","align.cwl","filtersort.cwl","dedup.cwl","count.cwl"],
    "cwl_version": "v1",
    "input_files": {
      "fastq": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_INPUT_FASTQ>"
      },
      "bwaIndex": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_INPUT_TGZ_BWA_INDEX>"
      },
      "chromsizes": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_CHROMSIZES_FILE>"
      }
    },
    "input_parameters": { "nthreads": 8 },
    "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
    "output_target": {
       "filtered_sorted_deduped_bam": "<YOUR_OUTPUT_FILTERED_BAM>.bam",
       "dedup_qc_report": "<YOUR_QC_REPORT>.zip",
       "count_bg": "<YOUR_OUTPUT_COUNT_BEDGRAPH_FILE>.bg"
    }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}

ChIP-seq data processing & QC

  • Example full pipeline run

chipseq_4dn_run

encode-chipseq-aln-chip

chipseq_aln_chip_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
  "args": {
    "app_name": "encode-chipseq-aln-chip",
    "app_version": "v1.1.1",
    "wdl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/chip-seq-pipeline2/4dn-v1.1.1/",
    "wdl_main_filename": "chip.wdl",
    "language": "wdl",
    "input_files": {
      "chip.fastqs": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": [[
            ["<YOUR_INPUT_FASTQ_R1_TECHREP1>.fastq.gz", "<YOUR_INPUT_FASTQ_R2_TECHREP1>.fastq.gz"],
            ["<YOUR_INPUT_FASTQ_R1_TECHREP2>.fastq.gz", "<YOUR_INPUT_FASTQ_R2_TECHREP2>.fastq.gz"]
        ]]
      },
      "chip.bwa_idx_tar": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "rename": "GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.tar",
        "object_key": "<YOUR_INPUT_TAR_BWA_INDEX>"
      },
      "chip.blacklist": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_BLACKLIST_FILE>.bed.gz"
      },
      "chip.chrsz": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_CHROMSIZES_FILE>.chrom.sizes"
      }
    },
    "input_parameters": {
        "chip.pipeline_type" : "histone",
        "chip.paired_end" : true,
        "chip.choose_ctl.always_use_pooled_ctl" : true,
        "chip.qc_report.name" : "<YOUR_QC_REPORT_NAME>",
        "chip.qc_report.desc" : "<YOUR_QC_REPORT_DESCRIPTION>",
        "chip.gensz" : "hs",
        "chip.bam2ta.regex_grep_v_ta" : "chr[MUE]|random|alt",
        "chip.fraglen": [],
        "chip.bwa.cpu": 16,
        "chip.merge_fastq.cpu": 16,
        "chip.filter.cpu": 16,
        "chip.bam2ta.cpu": 16,
        "chip.xcor.cpu": 16,
        "chip.align_only": true
    },
    "output_S3_bucket": "<YOUR_INPUT_BUCKET>",
    "output_target": {
       "chip.first_ta": "<YOUR_OUTPUT_TAG_ALIGN_FILE>.bed.gz",
       "chip.first_ta_xcor": "<YOUR_OUTPUT_TAG_ALIGN_FILE_FOR_XCOR>.bed.gz"
    }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}

encode-chipseq-aln-ctl

chipseq_aln_ctl_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
  "args": {
    "app_name": "encode-chipseq-aln-ctl",
    "app_version": "v1.1.1",
    "wdl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/chip-seq-pipeline2/4dn-v1.1.1/",
    "wdl_main_filename": "chip.wdl",
    "language": "wdl",
    "input_files": {
      "chip.ctl_fastqs": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": [[
            ["<YOUR_INPUT_FASTQ_R1_TECHREP1>.fastq.gz", "<YOUR_INPUT_FASTQ_R2_TECHREP1>.fastq.gz"],
            ["<YOUR_INPUT_FASTQ_R1_TECHREP2>.fastq.gz", "<YOUR_INPUT_FASTQ_R2_TECHREP2>.fastq.gz"]
        ]]
      },
      "chip.bwa_idx_tar": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "rename": "GRCh38_no_alt_analysis_set_GCA_000001405.15.fasta.tar",
        "object_key": "<YOUR_INPUT_TAR_BWA_INDEX>"
      },
      "chip.blacklist": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_BLACKLIST_FILE>.bed.gz"
      },
      "chip.chrsz": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_CHROMSIZES_FILE>.chrom.sizes"
      }
    },
    "input_parameters": {
        "chip.pipeline_type" : "histone",
        "chip.paired_end" : true,
        "chip.choose_ctl.always_use_pooled_ctl" : true,
        "chip.qc_report.name" : "<YOUR_QC_REPORT_NAME>",
        "chip.qc_report.desc" : "<YOUR_QC_REPORT_DESCRIPTION>",
        "chip.gensz" : "hs",
        "chip.bam2ta_ctl.regex_grep_v_ta" : "chr[MUE]|random|alt",
        "chip.fraglen": [],
        "chip.bwa_ctl.cpu": 16,
        "chip.merge_fastq_ctl.cpu": 16,
        "chip.filter_ctl.cpu": 16,
        "chip.bam2ta_ctl.cpu": 16,
        "chip.align_only": true
    },
    "output_S3_bucket": "<YOUR_INPUT_BUCKET>",
    "output_target": {
       "chip.first_ta": "<YOUR_OUTPUT_TAG_ALIGN_FILE>.bed.gz",
       "chip.first_ta_xcor": "<YOUR_OUTPUT_TAG_ALIGN_FILE_FOR_XCOR>.bed.gz"
    }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}

encode-chipseq-postaln

chipseq_postaln_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
    "args": {
      "app_name": "encode-chipseq-postaln",
      "app_version": "v1.1.1",
      "wdl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/chip-seq-pipeline2/4dn-v1.1.1/",
      "wdl_main_filename": "chip.wdl",
      "language": "wdl",
      "input_files" : {
         "chip.tas" : {
           "bucket_name": "<YOUR_INPUT_BUCKET>",
           "object_key": ["<YOUR_INPUT_TAG_ALIGN_BIOREP1>.bed.gz",
                          "<YOUR_INPUT_TAG_ALIGN_BIOREP2>.bed.gz"],
           "rename": ["<YOUR_INPUT_TAG_ALIGN_BIOREP1>.tagAlign.gz",
                      "<YOUR_INPUT_TAG_ALIGN_BIOREP2>.tagAlign.gz"]
         },
         "chip.ctl_tas" : {
           "bucket_name": "<YOUR_INPUT_BUCKET>",
           "object_key": ["<YOUR_INPUT_CTL_TAG_ALIGN_BIOREP1>.bed.gz",
                          "<YOUR_INPUT_CTL_TAG_ALIGN_BIOREP2>.bed.gz"],
           "rename": ["<YOUR_INPUT_CTL_TAG_ALIGN_BIOREP1>.tagAlign.gz",
                      "<YOUR_INPUT_CTL_TAG_ALIGN_BIOREP2>.tagAlign.gz"]
         },
         "chip.bam2ta_no_filt_R1.ta" : {
           "bucket_name": "<YOUR_INPUT_BUCKET>",
           "object_key": ["<YOUR_INPUT_XCOR_TAG_ALIGN_BIOREP1>.bed.gz",
                          "<YOUR_INPUT_XCOR_TAG_ALIGN_BIOREP1>.bed.gz"],
           "rename": ["<YOUR_INPUT_XCOR_TAG_ALIGN_BIOREP1>.tagAlign.gz",
                      "<YOUR_INPUT_XCOR_TAG_ALIGN_BIOREP2>.tagAlign.gz"]
         },
         "chip.blacklist" : {
           "bucket_name": "<YOUR_INPUT_BUCKET>",
           "object_key": "<YOUR_BLACKLIST_FILE>.bed.gz"
         },
         "chip.chrsz" : {
           "bucket_name": "<YOUR_INPUT_BUCKET>",
           "object_key": "<YOUR_CHROMSIZES_FILE>"
         }
      },
      "input_parameters": {
        "chip.pipeline_type" : "histone",
        "chip.paired_end" : true,
        "chip.choose_ctl.always_use_pooled_ctl" : true,
        "chip.qc_report.name" : "<YOUR_QC_REPORT_NAME>",
        "chip.qc_report.desc" : "<YOUR_QC_REPORT_DESCRIPTION>",
        "chip.gensz" : "hs",
        "chip.xcor.cpu": 4,
        "chip.spp_cpu": 4
      },
      "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
      "output_target": {
        "chip.sig_fc": "<YOUR_OUTPUT_SIGNAL_FC_FILE>.bw",
        "chip.optimal_peak": "<YOUR_OUTPUT_OPTIMAL_PEAK_FILE>.bb",
        "chip.conservative_peak": "<YOUR_OUTPUT_CONSERVATIVE_PEAK_FILE>.bb",
        "chip.report": "<YOUR_OUTPUT_QC_REPORT>.html",
        "chip.qc_json": "<YOUR_OUTPUT_QC_JSON>.json"
      }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}

ATAC-seq data processing & QC

  • Example full pipeline run

atacseq_4dn_run

encode-atacseq-aln

atacseq_aln_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
  "args": {
    "app_name": "encode-atacseq-aln",
    "app_version": "1.1.1",
    "wdl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/atac-seq-pipeline/4dn-v1.1.1/",
    "wdl_main_filename": "atac.wdl",
    "language": "wdl",
    "input_files": {
      "atac.bowtie2_idx_tar": {
        "rename": "mm10_no_alt_analysis_set_ENCODE.fasta.tar",
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_TAR_BOWTIE2_INDEX>"
      },
      "atac.fastqs": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": [[
            ["<YOUR_INPUT_FASTQ_R1_TECHREP1>.fastq.gz", "<YOUR_INPUT_FASTQ_R2_TECHREP1>.fastq.gz"],
            ["<YOUR_INPUT_FASTQ_R1_TECHREP2>.fastq.gz", "<YOUR_INPUT_FASTQ_R2_TECHREP2>.fastq.gz"]
        ]]
      },
      "atac.blacklist": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_BLACKLIST_FILE>.bed.gz"
      },
      "atac.chrsz": {
        "bucket_name": "<YOUR_INPUT_BUCKET>",
        "object_key": "<YOUR_CHROMSIZES_FILE>"
      }
    },
    "input_parameters": {
      "atac.trim_adapter.cpu": 4,
      "atac.paired_end": true,
      "atac.bam2ta.regex_grep_v_ta": "chr[MUE]|random|alt",
      "atac.enable_xcor": false,
      "atac.disable_ataqc": true,
      "atac.filter.cpu": 4,
      "atac.trim_adapter.auto_detect_adapter": true,
      "atac.bam2ta.cpu": 4,
      "atac.bowtie2.cpu": 4,
      "atac.gensz": "mm",
      "atac.pipeline_type": "atac",
      "atac.align_only": true
    },
    "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
    "output_target": {
      "atac.first_ta": "<YOUR_OUTPUT_TAGALIGN>.bed.gz",
      "atac.report": "<YOUR_OUTPUT_QC_REPORT>.html",
      "atac.qc_json": "<YOUR_OUTPUT_QC_JSON.json",
    }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}

encode-atacseq-postaln

atacseq_postaln_4dn_wf

  • Example input execution json template :

Use the following as a template and replace <YOUR....> with your input/output/log bucket/file(object) information.

{
    "args": {
      "app_name": "encode-atacseq-postaln",
      "app_version": "v1.1.1",
      "wdl_directory_url": "https://raw.githubusercontent.com/4dn-dcic/atac-seq-pipeline/4dn-v1.1.1/",
      "wdl_main_filename": "atac.wdl",
      "language": "wdl",
      "input_files" : {
         "atac.tas" : {
           "bucket_name": "<YOUR_INPUT_BUCKET>",
           "object_key": ["<YOUR_INPUT_TAG_ALIGN_BIOREP1>.bed.gz",
                          "<YOUR_INPUT_TAG_ALIGN_BIOREP2>.bed.gz"],
           "rename": ["<YOUR_INPUT_TAG_ALIGN_BIOREP1>.tagAlign.gz",
                      "<YOUR_INPUT_TAG_ALIGN_BIOREP2>.tagAlign.gz"]
         },
         "atac.blacklist" : {
           "bucket_name": "<YOUR_INPUT_BUCKET>",
           "object_key": "<YOUR_BLACKLIST_FILE>.bed.gz"
         },
         "atac.chrsz" : {
           "bucket_name": "<YOUR_INPUT_BUCKET>",
           "object_key": "<YOUR_CHROMSIZES_FILE>"
         }
      },
      "input_parameters": {
        "atac.pipeline_type" : "atac",
        "atac.paired_end" : true,
        "atac.gensz" : "hs",
        "atac.disable_ataqc": true,
        "atac.enable_xcor": false
      },
      "output_S3_bucket": "<YOUR_OUTPUT_BUCKET>",
      "output_target": {
        "atac.sig_fc": "<YOUR_OUTPUT_SIGNAL_FC_FILE>.bw",
        "atac.optimal_peak": "<YOUR_OUTPUT_OPTIMAL_PEAK_FILE>.bb",
        "atac.conservative_peak": "<YOUR_OUTPUT_CONSERVATIVE_PEAK_FILE>.bb",
        "atac.report": "<YOUR_OUTPUT_QC_REPORT>.html",
        "atac.qc_json": "<YOUR_OUTPUT_QC_JSON>.json"
      }
  },
  "config": {
    "log_bucket": "<YOUR_LOG_BUCKET>",
    "key_name": "<YOUR_KEY_NAME>"
  }
}