Description

Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

PacBio BAM file

*.bam

index{:bash}

:file

PacBio BAM file index (.pbi)

*.pbi

Output

name:type
description
pattern

fastq{:bash}

meta{:bash}

:map

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

*.fastq.gz{:bash}

:file

Gzipped FASTQ file

*.fastq.gz

versions_bam2fastx{:bash}

${task.process}{:bash}

:string

The name of the process

bam2fastx{:bash}

:string

The name of the tool

bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

bam2fastx{:bash}

:string

The name of the tool

bam2fastq --version 2>&1) | sed 's/^.*bam2fastq //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

bam2fastx
BSD-3-clause-Clear

Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files

github.com/PacificBiosciences/bam2fastx
maintainers
Github user priyanka-surana
Github user muffato
get in touch
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