run_macs2: Perform peakcalling with MACS2
In anilchalisey/chompR: ChIP and ATAC-seq data processing pipeline

Perform peakcalling with MACS2

run_macs2(macs2 = "macs2", out.dir = "peaks", treatment.files = NULL,
  control.files = NULL, input.format = "AUTO", broad = FALSE,
  species = c("human", "mouse"), sample.names = NULL,
  no.model = FALSE, extsize = 0, shift = 0, no.lambda = FALSE,
  call.summits = TRUE, qvalue = 0.05, verbosity = 3,
  threads = NULL)

`macs2`	character string specifying path to macs2 [DEFAULT = "macs2"]
`out.dir`	character string specifying the directory to which results will be saved. If the directory does not exist, it will be created. [DEFAULT = "peaks"]
`treatment.files`	character vector specifying path to alignment files. [DEFAULT = NULL]
`control.files`	character vector specifying path to input controls. This is optional, but if used then MUST be same length as <treatment.files>, so if the same input control is used for multiple ltreatments, then it should be specified multiple times. If NULL, then no.lambda will be set to `TRUE`. [DEFAULT = NULL]
`input.format`	character vector specifying format of input file; can be "ELAND", "BED", "ELANDMULTI", "ELANDEXPORT", "ELANDMULTIPET" (for pair-end tags), "SAM", "BAM", "BOWTIE", "BAMPE" or "BEDPE". [DEFAULT = "AUTO"]
`broad`	logical, if TRUE then MACS2 will output broadpeak results
`species`	character string specifying the name of the species. Only `'human'`, and `'mouse'` are supported at present. [DEFAULT = human].
`sample.names`	character vector specifying sample names to use as prefix for files. If NULL, this will be derived from the file names. [DEFAULT = NULL]
`no.model`	logical, if TRUE then MACS2 shifting model will be bypassed.
`extsize`	numeric vector. If no.model = TRUE, this parameter is to extend reads in 5'->3' direction to fix-sized fragments. Ignored if no.model = FALSE or paired end reads. If used, MUST be same length as <treatment.files> and in same order. [DEFAULT = 0]
`shift`	numeric vector. If no.model = TRUE, this value is used to move cutting ends (5') then apply extsize from 5' to 3' direction to extend them to fragments. When this value is negative, ends will be moved toward 3'->5' direction, otherwise 5'->3' direction. [DEFAULT = 0]
`no.lambda`	logical, if TRUE then the background lambda will be used as local lambda.
`call.summits`	logical, if TRUE then MACS2 will reanalyze the shape of signal profile to deconvolve subpeaks within each peak. If used, the output subpeaks of a big peak region will have the same peak boundaries, but different scores and peak summit positions. [DEFAULT = TRUE]
`qvalue`	numeric value specifying the minimum FDR cutoff to call significant regions. [DEFAULT = 0.05]
`verbosity`	integer value specifying verbosity. If 0 then only critical messages displayed. If greater or equal to 3 then all messages shown.
`threads`	an integer value indicating the number of workers to be used. If NULL then one less than the maximum number of cores will be used. [DEFAULT = NULL].