bwa.yaml

{
  id: bwa,
  name: BWA (Burrows-Wheeler Alignment Tool),
  article: 10.1093/bioinformatics/btp324,
  website: "http://bio-bwa.sourceforge.net/",
  git: "https://github.com/lh3/bwa",
  description: "BWA is a software package for mapping low-divergent sequences against a large reference genome.",
  version: "0.7.17",
  documentation: "http://bio-bwa.sourceforge.net/bwa.shtml",
  multiqc: "custom",
  commands:
    [
      {
        name: bwa_index,
        command: bwa index,
        output_dir: bwa/index,
        inputs: [{ name: bwa_index_genome_fasta , file: ""}],
        outputs: [{ name: index, file: index, description: "Index files for bwa alignment" }],
        options:
          [
            {
              name: bwa_index_path,
              type: input_dir,
              value: "",
              label: "Path to an existing bwa index (or where to save a new one)",
            },
            {
              name: bwa_index_genome_fasta,
              type: input_file,
              accept: [".fasta",".fa",".fasta.gz",".fa.gz"],
              value: "",
              multiple: FALSE,
              label: "Path to reference genome fasta file",
            },
            {
              name: "bwa_index_algorithm",
              type: "radio",
              value: "bwtsw",
              choices: [bwtsw: bwtsw, is: is],
              label: "Algorithm for constructing BWT index (see documentation for details)",
            }
          ]
      },
      {
        name: bwa_mem_PE,
        command: bwa mem,
        output_dir: bwa/mem/PE,
        inputs: [{ name: reads }, { name: index, file: bwa/index/index }],
        outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
        options:
          [
            {
              name: bwa_mem_threads,
              prefix: -t,
              type: numeric,
              value: 4,
              min: 1,
              max: NA,
              step: 1,
              label: "Number of threads to use",
            },
            {
              name: bwa_mem_quality0_multimapping,
              prefix: ,
              type: checkbox,
              value: TRUE,
              label: "Put 0 as mapping quality for multimapping reads",
            }
          ]
      },
      {
        name: bwa_mem_SE,
        command: bwa mem,
        output_dir: bwa/mem/SE,
        inputs: [{ name: reads }, { name: index, file: bwa/index/index }],
        outputs: [{ name: bam, file: "{sample}.bam", description: "Alignment files" }],
        options:
          [
            {
              name: bwa_mem_threads,
              prefix: -t,
              type: numeric,
              value: 4,
              min: 1,
              max: NA,
              step: 1,
              label: "Number of threads to use",
            },
            {
              name: bwa_mem_quality0_multimapping,
              prefix: ,
              type: checkbox,
              value: TRUE,
              label: "Put 0 as mapping quality for multimapping reads",
            }
          ]
      }
    ],
  install:  {
    bwa: [
      "cd /opt/biotools",
      "wget https://github.com/lh3/bwa/releases/download/v0.7.17/bwa-0.7.17.tar.bz2",
      "tar -xvjf bwa-0.7.17.tar.bz2",
      "cd bwa-0.7.17",
      "make -j 10",
      "mv bwa ../bin/",
      "cd ..",
      "rm -r bwa-0.7.17 bwa-0.7.17.tar.bz2"
    ],
    samtools: [
      "cd /opt/biotools",
      "wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2",
      "tar -xvjf samtools-1.9.tar.bz2",
      "cd samtools-1.9",
      "./configure && make",
      "cd ..",
      "mv samtools-1.9/samtools bin/samtools",
      "rm -r samtools-1.9 samtools-1.9.tar.bz2"
    ]
  },
  citations: [
    bwa: [
      "Heng Li, Richard Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform, Bioinformatics, Volume 25, Issue 14, 15 July 2009, Pages 1754–1760, https://doi.org/10.1093/bioinformatics/btp324"
    ],
    bwa-mem: [
      "Li H. (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v1 [q-bio.GN]"
    ],
    samtools: [
      "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078–2079, https://doi.org/10.1093/bioinformatics/btp352"
    ]
  ]
}