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:map

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

bam:file

BAM file

*.bam

Output

name:type
description
pattern

fastq

meta:map

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

**/*.fastq.gz:file

fastq compressed file

**/*.fastq.gz

versions

versions.yml:file

File containing software versions

versions.yml

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
Github user BlueBicycleBlog
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