"help_text":"By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
}
}
},
"hicstuff options":{
"title":"Hicstuff options",
"type":"object",
"description":"Options for hicstuff workflow, set in the config file.",
"help_text":"These options are specific to the hicstuff workflow and allow you to customise the parameters",
"properties":{
"workflow":{
"type":"string",
"description":"Selection of the workflow to run. Choices are hicstuff or hicpro",
"default":"hicstuff",
"fa_icon":"fas fa-cogs"
},
"hicstuff_bwt2_align_opts":{
"type":"string",
"description":"Parameters for bowtie2 alignment",
"default":"--very-sensitive-local",
"fa_icon":"fas fa-cogs"
},
"hicstuff_min_size":{
"type":"integer",
"description":"Minimum contig size required to keep it",
"default":0,
"fa_icon":"fas fa-cogs"
},
"hicstuff_min_qual":{
"type":"integer",
"description":"Minimum mapping quality required to keep a pair of Hi-C reads",
"default":30,
"fa_icon":"fas fa-cogs"
},
"hicstuff_circular":{
"type":"boolean",
"description":"Use if the genome is circular",
"default":false,
"fa_icon":"fas fa-cogs"
},
"hicstuff_bin":{
"type":"integer",
"description":"Binsize for plotting matrix",
"default":10000,
"fa_icon":"fas fa-cogs"
},
"hicstuff_output_contigs":{
"type":"string",
"description":"Name of info contigs file",
"default":"info_contigs.txt",
"fa_icon":"fas fa-cogs"
},
"hicstuff_output_frags":{
"type":"string",
"description":"Name of fragments list file",
"default":"fragments_list.txt",
"fa_icon":"fas fa-cogs"
},
"hicstuff_valid_pairs":{
"type":"string",
"description":"Name of valid pairs file",
"default":"valid.pairs",
"fa_icon":"fas fa-cogs"
},
"hicstuff_valid_idx":{
"type":"string",
"description":"Name of valid pairs index file",
"default":"valid_idx.pairs",
"fa_icon":"fas fa-cogs"
},
"hicstuff_matrix":{
"type":"string",
"description":"Common name of matrix files",
"default":"abs_fragments_contacts_weighted.txt",
"fa_icon":"fas fa-cogs"
},
"hicstuff_plot_events":{
"type":"boolean",
"description":"Whether plots should be generated at different steps of the pipeline",
"default":false,
"fa_icon":"fas fa-cogs"
},
"hicstuff_frags_plot":{
"type":"boolean",
"description":"Whether fragments plot should be generated",
"default":"false",
"fa_icon":"fas fa-cogs"
},
"hicstuff_frags_plot_path":{
"type":"string",
"description":"Name of fragments plot file",
"default":"frag_hist.pdf",
"fa_icon":"fas fa-cogs"
},
"hicstuff_pie_plot":{
"type":"string",
"description":"Prefix of distribution plot file during filter events",
"default":"distrib",
"fa_icon":"fas fa-cogs"
},
"hicstuff_dist_plot":{
"type":"string",
"description":"Prefix of distance plot file during filter events",
"default":"dist",
"fa_icon":"fas fa-cogs"
},
"distance_law":{
"type":"boolean",
"description":"If True, generates a distance law file with the values of the probabilities to have a contact between two distances for each chromosomes or arms if the file with the positions has been given. The values are not normalized, or averaged.",
"default":"false",
"fa_icon":"fas fa-cogs"
},
"hicstuff_distance_out_file":{
"type":"string",
"description":"Name of distance law table file",
"default":"distance_law.txt",
"fa_icon":"fas fa-cogs"
},
"hicstuff_distance_plot":{
"type":"boolean",
"description":"Whether distance law table should be plotted",
"default":"false",
"fa_icon":"fas fa-cogs"
},
"hicstuff_distance_out_plot":{
"type":"string",
"description":"Name of distance law table plot if hicstuff_distance_plot is true",
"default":"distance_law.txt",
"fa_icon":"fas fa-cogs"
},
"hicstuff_base":{
"type":"number",
"description":"Base use to construct the logspace of the bins for distance law",
"default":1.1,
"fa_icon":"fas fa_cogs"
},
"hicstuff_rm_centro":{
"type":"string",
"description":"If the distance law is computed, this is the number of kb that will be removed around the centromere position given by in the centromere file",
"default":"None",
"fa_icon":"fas fa-cogs"
},
"hicstuff_centro_file":{
"type":"string",
"description":"If not None, path of file with Positions of the centromeres separated by aspace and in the same order than the chromosomes",
"default":"None",
"fa_icon":"fas fa_cogs"
},
"filter_event":{
"type":"boolean",
"description":"Filter spurious or uninformative 3C events. Requires a restriction enzyme",
"default":"false",
"fa_icon":"fas fa-cogs"
},
"hicstuff_valid_idx_filtered":{
"type":"string",
"description":"Name of filtered valid pairs index file",
"default":"valid_idx_filtered.pairs",
"fa_icon":"fas fa-cogs"
},
"filter_pcr":{
"type":"boolean",
"description":"If True, PCR duplicates will be filtered based on genomic positions Pairs where both reads have exactly the same coordinates are considered duplicates and only one of those will be conserved.",
"default":"false",
"fa_icon":"fas fa-cogs"
},
"hicstuff_filter_pcr_out_file":{
"type":"string",
"description":"Name of pair file after PCR filtering",
