modules/fgbio_fastqtobam

Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads

unalignedbamcram

Description

Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads

Name (Type)

Description

Pattern

pair of reads to be converted into BAM file

*.{fastq.gz}

Name (Type)

Description

Pattern

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

File containing software version

*.{version.yml}

Unaligned, unsorted BAM file

*.{bam}

Unaligned, unsorted CRAM file

*.{cram}

A set of tools for working with genomic and high throughput sequencing data, including UMIs