htseq_count.yaml

{
  id: htseq_count,
  name: Htseq_count,
  article: doi:10.1093/bioinformatics/btu638,
  website: "https://htseq.readthedocs.io",
  git: "https://github.com/htseq/htseq",
  description: "A tool to quantify gene expression in RNA-Seq and similar experiments.",
  version: "release_0.13.5",
  documentation: "https://htseq.readthedocs.io",
  multiqc: "htseq",
  commands:
    [
      {
        name: htseq_count,

        command: htseq-count,
        category: "quantification",
        output_dir: htseq_count,
        inputs: [
          { name: bam, type: "bams" },
          { name: gff_file, type: "gff3"}
        ],
        outputs:
          [
            { name: stats, type: "txt", file: "{sample}_htseq_count.txt", description: "a table with counts for each feature" }
          ],
        options:
          [
            {
              name: htseq_count_minaqual,
              prefix: -a,
              type: numeric,
              value: 10,
              min: 1,
              max: 80,
              step: 1,
              label: "skip all reads with alignment quality lower than the given minimum value",
            },
            {
              name: htseq_stranded,
              type: radio,
              choices:
                [
                  Not stranded: "no",
                  Stranded: "yes",
                  Reverse Stranded: "reverse",
                ],
              value: "no",
              label: "whether the data is from a strand-specific assay.",
            },
            {
              name: htseq_orientation,
              type: radio,
              choices:
                [
                  Position: "pos",
                  Name: "name"
                ],
              value: "position",
              label: "the way that alignment have been sorted (either by read name or by alignment position).",
            },
          ],
      },
    ],
  install: { 
    htseq: [
      "pip3 install 'HTSeq==0.13.5' ",
    ]
  },
  citations:  {
    htseq: [
      "Simon Anders, Paul Theodor Pyl, Wolfgang Huber. HTSeq - A Python framework to work with high-throughput sequencing data Bioinformatics (2014)."
    ]
  }
}