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{
"class": "Workflow",
"cwlVersion": "v1.0",
"fdn_meta": {
"category": "merging + aggregation + normalization",
"data_types": [
"Hi-C"
],
"description": "This is a subworkflow of the Hi-C data analysis pipeline. It takes pairs files for all replicates of a sample, merges them and then produces multi-resolution Hi-c matrices for visualization. The pipeline produces 4 output files. 1) Replicated merged pairs file 2) Contact matrices in .hic format 3) Multiresolution mcool file and 4) normalization vector of mcool files for visualization in juicebox.",
"name": "hi-c-processing-pairs",
"title": "Generation of multiresolution Hi-C contact matrices from a set of contact lists",
"workflow_type": "Hi-C data analysis"
},
"inputs": [
{
"fdn_format": "pairs",
"id": "#input_pairs",
"type": [
"null",
{
"items": "File",
"type": "array"
}
]
},
{
"fdn_format": "chromsize",
"id": "#chromsizes",
"type": [
"File"
]
},
{
"fdn_format": "juicer_format_restriction_site_file",
"id": "#restriction_file",
"type": [
"null",
"File"
]
},
{
"default": 8,
"id": "#nthreads",
"type": [
"int"
]
},
{
"default": 1000,
"id": "#min_res",
"type": [
"int"
]
},
{
"default": "14g",
"id": "#maxmem",
"type": [
"string"
]
},
{
"default": false,
"id": "#higlass",
"type": [
"boolean"
]
},
{
"default": false,
"id": "#juicer_res",
"type": [
"boolean"
]
},
{
"default": "1000,2000,5000,10000,25000,50000,100000,250000,500000,1000000,2500000,5000000,10000000",
"id": "#custom_res",
"type": [
"string"
]
},
{
"default": 13,
"id": "#nres",
"type": [
"int"
]
},
{
"default": 10000000,
"id": "#chunksize",
"type": [
"int"
]
},
{
"default": 0,
"id": "#mapqfilter_juicer",
"type": [
"int"
]
},
{
"default": 2,
"id": "#max_split_cooler",
"type": [
"int"
]
},
{
"default": false,
"id": "#nofrag",
"type": [
"boolean"
]
}
],
"outputs": [
{
"fdn_format": "pairs",
"fdn_output_type": "processed",
"fdn_secondary_file_formats": [
"pairs_px2"
],
"id": "#merged_pairs",
"outputSource": "#merge-pairs/merged_pairs",
"type": [
"File"
]
},
{
"fdn_format": "hic",
"fdn_output_type": "processed",
"id": "#hic",
"outputSource": "#pairs2hic/hic",
"type": [
"File"
]
},
{
"fdn_format": "mcool",
"fdn_output_type": "processed",
"id": "#mcool",
"outputSource": "#add-hic-normvector-to-mcool/mcool_with_hicnorm",
"type": [
"File"
]
},
{
"fdn_format": "normvector_juicerformat",
"fdn_output_type": "processed",
"id": "#cooler_normvector",
"outputSource": "#extract-mcool-normvector-for-juicebox/cooler_normvector",
"type": [
"File"
]
}
],
"requirements": [
{
"class": "ScatterFeatureRequirement"
},
{
"class": "InlineJavascriptRequirement"
}
],
"steps": [
{
"fdn_step_meta": {
"analysis_step_types": [
"merging"
],
"description": "Merging pair files",
"software_used": [
"pairix_0.3.3"
]
},
"id": "#merge-pairs",
"in": [
{
"arg_name": "input_pairs",
"fdn_cardinality": "array",
"fdn_format": "pairs",
"fdn_type": "data file",
"id": "#merge-pairs/input_pairs",
"source": "#input_pairs"
}
],
"out": [
{
"arg_name": "merged_pairs",
"fdn_cardinality": "single",
"fdn_format": "pairs",
"fdn_type": "data file",
"id": "#merge-pairs/merged_pairs"
}
],
"run": "merge-pairs.cwl"
},
{
"fdn_step_meta": {
"analysis_step_types": [
"annotation"
],
"description": "Adding restriction enzyme site information to the pairs file",
"software_used": [
"pairix_0.3.3"
]
},
"id": "#addfragtopairs",
"in": [
{
"arg_name": "input_pairs",
"fdn_cardinality": "single",
"fdn_format": "pairs",
"fdn_type": "data file",
"id": "#addfragtopairs/input_pairs",
"source": "#merge-pairs/merged_pairs"
},
{
"arg_name": "restriction_file",
"fdn_cardinality": "single",
"fdn_format": "juicer_format_restriction_site_file",
"fdn_type": "reference file",
"id": "#addfragtopairs/restriction_file",
"source": "#restriction_file"
},
{
"arg_name": "donothing",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#addfragtopairs/donothing",
"source": "#nofrag"
}
],
"out": [
{
"arg_name": "pairs_with_frags",
"fdn_cardinality": "single",
"fdn_format": "pairs",
"fdn_type": "data file",
"id": "#addfragtopairs/pairs_with_frags"
}
],
"run": "addfragtopairs.cwl"
},
{
"fdn_step_meta": {
"analysis_step_types": [
"aggregation"
],
"description": "Merged Pairs file is processed using Cooler",
"software_used": [
"cooler_0.7.6"
]
},
"id": "#cooler",
"in": [
{
"arg_name": "pairs",
"fdn_cardinality": "single",
"fdn_format": "pairs",
"fdn_type": "data file",
"id": "#cooler/pairs",
"source": "#merge-pairs/merged_pairs"
},
{
"arg_name": "chrsizes",
"fdn_cardinality": "single",
"fdn_format": "chromsizes",
"fdn_type": "reference file",
"id": "#cooler/chrsizes",
"source": "#chromsizes"
},
{
"arg_name": "binsize",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#cooler/binsize",
"source": "#min_res"
},
{
"arg_name": "ncores",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#cooler/ncores",
"source": "#nthreads"
},
{
"arg_name": "max_split",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#cooler/max_split",
"source": "#max_split_cooler"
}
],
"out": [
{
"arg_name": "cool",
"fdn_cardinality": "single",
"fdn_format": "cool",
"fdn_type": "data file",
"id": "#cooler/cool"
}
],
"run": "cooler.cwl"
},
{
"fdn_step_meta": {
"analysis_step_types": [
"aggregation",
"normalization"
],
"description": "Merged Pairs file is processed using Juicebox",
"software_used": [
"juicer_tools_1.8.9-cuda8"
]
},
"id": "#pairs2hic",
"in": [
{
"arg_name": "input_pairs",
"fdn_cardinality": "single",
"fdn_format": "pairs",
"fdn_type": "data file",
"id": "#pairs2hic/input_pairs",
"source": "#addfragtopairs/pairs_with_frags"
},
{
"arg_name": "chromsizes",
"fdn_cardinality": "single",
"fdn_format": "chromsizes",
"fdn_type": "reference file",
"id": "#pairs2hic/chromsizes",
"source": "#chromsizes"
},
{
"arg_name": "min_res",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#pairs2hic/min_res",
"source": "#min_res"
},
{
"arg_name": "higlass",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#pairs2hic/higlass",
"source": "#higlass"
},
{
"arg_name": "custom_res",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#pairs2hic/custom_res",
"source": "#custom_res"
},
{
"arg_name": "maxmem",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#pairs2hic/maxmem",
"source": "#maxmem"
},
{
"arg_name": "mapqfilter",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#pairs2hic/mapqfilter",
"source": "#mapqfilter_juicer"
}
],
"out": [
{
"arg_name": "hic",
"id": "#pairs2hic/hic"
}
],
"run": "pairs2hic.cwl"
},
{
"fdn_step_meta": {
"analysis_step_types": [
"aggregation",
"normalization",
"file format conversion"
],
"description": "Cooler file is converted to mcool",
"software_used": [
"cooler_0.7.6"
]
},
"id": "#cool2mcool",
"in": [
{
"arg_name": "input_cool",
"fdn_cardinality": "single",
"fdn_format": "cool",
"fdn_type": "data file",
"id": "#cool2mcool/input_cool",
"source": "#cooler/cool"
},
{
"arg_name": "ncores",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#cool2mcool/ncores",
"source": "#nthreads"
},
{
"arg_name": "chunksize",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#cool2mcool/chunksize",
"source": "#chunksize"
},
{
"arg_name": "juicer_res",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#cool2mcool/juicer_res",
"source": "#juicer_res"
},
{
"arg_name": "custom_res",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#cool2mcool/custom_res",
"source": "#custom_res"
}
],
"out": [
{
"arg_name": "mcool",
"fdn_cardinality": "single",
"fdn_format": "mcool",
"fdn_type": "data file",
"id": "#cool2mcool/mcool"
}
],
"run": "cool2mcool.cwl"
},
{
"fdn_step_meta": {
"analysis_step_types": [
"file format conversion"
],
"description": "HiC normalization vector is added to mcooler",
"software_used": [
"hic2cool_0.4.1"
]
},
"id": "#add-hic-normvector-to-mcool",
"in": [
{
"arg_name": "input_mcool",
"fdn_cardinality": "single",
"fdn_format": "mcool",
"fdn_type": "data file",
"id": "#add-hic-normvector-to-mcool/input_mcool",
"source": "#cool2mcool/mcool"
},
{
"arg_name": "input_hic",
"fdn_cardinality": "single",
"fdn_format": "hic",
"fdn_type": "data file",
"id": "#add-hic-normvector-to-mcool/input_hic",
"source": "#pairs2hic/hic"
}
],
"out": [
{
"arg_name": "mcool_with_hicnorm",
"fdn_cardinality": "single",
"fdn_format": "mcool",
"fdn_type": "data file",
"id": "#add-hic-normvector-to-mcool/mcool_with_hicnorm"
}
],
"run": "add-hic-normvector-to-mcool.cwl"
},
{
"fdn_step_meta": {
"analysis_step_types": [
"file format conversion"
],
"description": "Extracting HiC normalization vector",
"software_used": [
"mcool2hic_87a912"
]
},
"id": "#extract-mcool-normvector-for-juicebox",
"in": [
{
"arg_name": "custom_res",
"fdn_cardinality": "single",
"fdn_type": "parameter",
"id": "#extract-mcool-normvector-for-juicebox/custom_res",
"source": "#custom_res"
},
{
"arg_name": "chromsize",
"fdn_cardinality": "single",
"fdn_format": "chromsizes",
"fdn_type": "reference file",
"id": "#extract-mcool-normvector-for-juicebox/chromsize",
"source": "#chromsizes"
},
{
"arg_name": "mcool",
"fdn_cardinality": "single",
"fdn_format": "mcool",
"fdn_type": "data file",
"id": "#extract-mcool-normvector-for-juicebox/mcool",
"source": "#add-hic-normvector-to-mcool/mcool_with_hicnorm"
}
],
"out": [
{
"arg_name": "cooler_normvector",
"fdn_cardinality": "single",
"fdn_format": "normvector_juicerformat",
"fdn_type": "data file",
"id": "#extract-mcool-normvector-for-juicebox/cooler_normvector"
}
],
"run": "extract-mcool-normvector-for-juicebox.cwl"
}
]
}
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