Description

Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis

Input

name:type
description
pattern

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

bam{:bash}

:file

BAM file

*.bam

Output

name:type
description
pattern

fastq{:bash}

meta{:bash}

:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

**/*.fastq.gz{:bash}

:file

fastq compressed file

**/*.fastq.gz

versions_bamtofastq10x{:bash}

${task.process}{:bash}

:string

The name of the process

bamtofastq10x{:bash}

:string

The name of the tool

bamtofastq --version |& sed "1!d ; s/bamtofastq //"{: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

bamtofastq10x{:bash}

:string

The name of the tool

bamtofastq --version |& sed "1!d ; s/bamtofastq //"{:bash}

:eval

The expression to obtain the version of the tool

Tools

bamtofastq10x
MIT

Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis

github.com/10XGenomics/bamtofastq
maintainer
Github user BlueBicycleBlog
get in touch
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