bbmap_reformat
Description¶
Reformat and convert sequencing reads using BBMap's reformat.sh tool. Handles only single-end or merged FASTQ/FASTA files, adding unique names and trimming read descriptions.
Installation¶
ebi-metagenomics/bbmap/reformat
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install bbmap/reformat
Tools¶
bbmap¶
BBMap is a fast and memory-efficient aligner and toolkit for various bioinformatics operations, including read reformatting and validation.
- jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide
- sourceforge.net/projects/bbmap
- https://github.com/bbushnell/BBTools/blob/master/license.txt
Input¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Metadata dictionary containing sample identifier and single_end flag | id|single_end |
reads |
file | Input FASTQ file(s). Can be single-end or interleaved paired-end. | *.{fastq,fq,fastq.gz,fq.gz} |
out_fmt |
string | Output file format extension (e.g., 'fastq.gz', 'fasta.gz') | ^\w+(\.\w+)*$ |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Metadata passed through from input | - |
reformated |
file | Reformatted reads with unique names and trimmed descriptions. | *_reformated.{fastq,fq,fastq.gz,fq.gz,fasta,fa,fasta.gz,fa.gz} |
log |
file | BBMap reformat.sh log file | *.log |
versions |
file | File containing software versions | versions.yml |
