4.33. fastq_to_ubam

Convert reads from fastq format (single or paired) to unaligned BAM format.

4.33.1. Inputs

4.33.1.1. Required inputs

fastq_to_ubam.FastqToUBAM.fastq_1
File — Default: None
Unaligned read1 file in fastq format

fastq_to_ubam.FastqToUBAM.library_name
String — Default: None
Library name. This is required and will populate the 'LB' read group value. SM & LB combinations must be identical for any sequencing reads generated from the same sequencing library, and must be distinct for any reads generated from different libraries.

fastq_to_ubam.FastqToUBAM.platform_name
String — Default: None
Sequencing platform. This is required and will populate the 'PL' read group value. Must be one of CAPILLARY, DNBSEQ, HELICOS, ILLUMINA, IONTORRENT, LS454, ONT, PACBIO, or SOLID.

fastq_to_ubam.FastqToUBAM.sample_name
String — Default: None
Sample name. This is required and will populate the 'SM' read group value and will be used as the output filename (must be filename-friendly).

4.33.1.2. Other inputs

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fastq_to_ubam.FastqToUBAM.docker
String — Default: "quay.io/broadinstitute/viral-core:2.1.33"
???

fastq_to_ubam.FastqToUBAM.fastq_2
File? — Default: None
Unaligned read2 file in fastq format. This should be empty for single-end read conversion and required for paired-end reads. If provided, it must match fastq_1 in length and order.

fastq_to_ubam.FastqToUBAM.platform_unit
String? — Default: None
???

fastq_to_ubam.FastqToUBAM.readgroup_name
String? — Default: None
???

fastq_to_ubam.FastqToUBAM.run_date
String? — Default: None
???

fastq_to_ubam.FastqToUBAM.sequencing_center
String? — Default: None
???

4.33.2. Outputs

fastq_to_ubam.unmapped_bam
File
???

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