samtools_bam2fq
Description¶
The module uses bam2fq method from samtools to convert a SAM, BAM or CRAM file to FASTQ format
Pipelines¶
This module is used by the following pipelines:
Installation¶
ebi-metagenomics/samtools/bam2fq
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install samtools/bam2fq
Tools¶
samtools¶
Tools for dealing with SAM, BAM and CRAM files
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | - |
bam_file |
file | Sorted BAM file | - |
split |
boolean | True or false indicating whether the output is for single or paired-end reads | - |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] | - |
reads |
file | List of fastq files. Two files for paired-end reads and one file for single-end reads | - |
singleton_reads |
file | Fastq files generated for unpaired paired-end reads | - |
other_reads |
file | Other fastq files generated for paired-end reads | - |
versions |
file | File containing software versions | - |
