name: homer_maketagdirectory
description: Create a tag directory with the HOMER suite
keywords:
  - peaks
  - bed
  - bam
  - sam
tools:
  - homer:
      description: |
        HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis.
      documentation: http://homer.ucsd.edu/homer/
      doi: 10.1016/j.molcel.2010.05.004.
      licence: ["GPL-3.0-or-later"]
  - samtools:
      description: |
        SAMtools is a set of utilities for interacting with and post-processing
        short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
        These files are generated as output by short read aligners like BWA.
      homepage: http://www.htslib.org/
      documentation: hhttp://www.htslib.org/doc/samtools.html
      doi: 10.1093/bioinformatics/btp352
      licence: ["MIT"]
  - DESeq2:
      description: |
        Differential gene expression analysis based on the negative binomial distribution
      homepage: "https://bioconductor.org/packages/DESeq2"
      documentation: "https://bioconductor.org/packages/DESeq2"
      tool_dev_url: "https://github.com/mikelove/DESeq2"
      doi: 10.18129/B9.bioc.DESeq2
      licence: ["LGPL-3.0-or-later"]
  - edgeR:
      description: |
        Empirical Analysis of Digital Gene Expression Data in R
      homepage: "https://bioinf.wehi.edu.au/edgeR"
      documentation: "https://bioconductor.org/packages/edgeR"
      tool_dev_url: " https://git.bioconductor.org/packages/edgeR"
      doi: 10.18129/B9.bioc.edgeR
      licence: ["GPL >=2"]
input:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - bam:
      type: file
      description: BAM/BED/SAM file
      pattern: "*.{bam,bed,sam}"
  - fasta:
      type: file
      description: Fasta file of reference genome
      pattern: "*.fasta"
output:
  - meta:
      type: map
      description: |
        Groovy Map containing sample information
        e.g. [ id:'test', single_end:false ]
  - tagdir:
      type: directory
      description: The "Tag Directory"
      pattern: "*_tagdir"
  - taginfo:
      type: directory
      description: The tagInfo.txt included to ensure there's proper output
      pattern: "*_tagdir/tagInfo.txt"
  - versions:
      type: file
      description: File containing software versions
      pattern: "versions.yml"
authors:
  - "@EMiller88"
