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bwa_aln

description
Maps Single-End FASTQ files to BAM format using bwa aln
outputs
{'bam': 'Aligned BAM format file'}

Inputs

Required

  • _runtime (Any, required)
  • bwa_db_tar_gz (File, required): Gzipped tar archive of the bwa reference files. Files should be at the root of the archive.
  • fastq (File, required): Input FASTQ file to align with bwa

Defaults

  • modify_disk_size_gb (Int, default=0): Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
  • ncpu (Int, default=2); description: Number of cores to allocate for task; common: true
  • prefix (String, default=sub(basename(fastq),"([_\.][rR][12])?(\.subsampled)?\.(fastq|fq)(\.gz)?$","")): Prefix for the BAM file. The extension .bam will be added.
  • read_group (String, default=""); description: Read group information for BWA to insert into the header. BWA format: '@RG ID:foo SM:bar'; common: true
  • use_all_cores (Boolean, default=false); description: Use all cores? Recommended for cloud environments.; common: true

Outputs

  • bam (File)

bwa_aln_pe

description
Maps Paired-End FASTQ files to BAM format using bwa aln
outputs
{'bam': 'Aligned BAM format file'}

Inputs

Required

  • _runtime (Any, required)
  • bwa_db_tar_gz (File, required): Gzipped tar archive of the bwa reference files. Files should be at the root of the archive.
  • read_one_fastq_gz (File, required); description: Input gzipped FASTQ read one file to align with bwa; stream: false
  • read_two_fastq_gz (File, required); description: Input gzipped FASTQ read two file to align with bwa; stream: false

Defaults

  • modify_disk_size_gb (Int, default=0): Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
  • ncpu (Int, default=4); description: Number of cores to allocate for task; common: true
  • prefix (String, default=sub(basename(read_one_fastq_gz),"([_\.][rR][12])?(\.subsampled)?\.(fastq|fq)(\.gz)?$","")): Prefix for the BAM file. The extension .bam will be added.
  • read_group (String, default=""); description: Read group information for BWA to insert into the header. BWA format: '@RG ID:foo SM:bar'; common: true
  • use_all_cores (Boolean, default=false); description: Use all cores? Recommended for cloud environments.; common: true

Outputs

  • bam (File)

bwa_mem

description
Maps FASTQ files to BAM format using bwa mem
outputs
{'bam': 'Aligned BAM format file'}

Inputs

Required

  • _runtime (Any, required)
  • bwa_db_tar_gz (File, required): Gzipped tar archive of the bwa reference files. Files should be at the root of the archive.
  • read_one_fastq_gz (File, required): Input gzipped FASTQ read one file to align with bwa

Optional

  • read_two_fastq_gz (File?): Input gzipped FASTQ read two file to align with bwa

Defaults

  • modify_disk_size_gb (Int, default=0): Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.
  • ncpu (Int, default=4); description: Number of cores to allocate for task; common: true
  • prefix (String, default=sub(basename(read_one_fastq_gz),"([_\.][rR][12])?(\.subsampled)?\.(fastq|fq)(\.gz)?$","")): Prefix for the BAM file. The extension .bam will be added.
  • read_group (String, default=""); description: Read group information for BWA to insert into the header. BWA format: '@RG ID:foo SM:bar'; common: true
  • use_all_cores (Boolean, default=false); description: Use all cores? Recommended for cloud environments.; common: true

Outputs

  • bam (File)

build_bwa_db

description
Creates a BWA index and returns it as a compressed tar archive
outputs
{'bwa_db_tar_gz': 'Tarballed bwa reference files'}

Inputs

Required

  • _runtime (Any, required)
  • reference_fasta (File, required): Input reference Fasta file to index with bwa. Should be compressed with gzip.

Defaults

  • db_name (String, default="bwa_db"); description: Name of the output gzipped tar archive of the bwa reference files. The extension .tar.gz will be added.; common: true
  • modify_disk_size_gb (Int, default=0): Add to or subtract from dynamic disk space allocation. Default disk size is determined by the size of the inputs. Specified in GB.

Outputs

  • bwa_db_tar_gz (File)