bbmap_reformat_standardise
Description¶
De-interleave interleaved paired-end reads and standardize FASTQ format using BBMap's reformat.sh tool.
Installation¶
ebi-metagenomics/bbmap/reformat_standardise
nf-core modules -g https://www.github.com/ebi-metagenomics/nf-modules install bbmap/reformat/standardise
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, single_end flag, and interleaved flag | id|single_end|interleaved |
reads |
file | Input FASTQ file(s). Can be single-end or paired-end (as list). Paired-end reads can be interleaved (single file) or de-interleaved (two files). | *.{fastq,fq,fastq.gz,fq.gz} |
out_fmt |
string | Output file format (e.g., 'fastq.gz', 'fasta.gz') | ^\w+(\.\w+)*$ |
Output¶
| Name | Type | Description | Pattern |
|---|---|---|---|
meta |
map | Metadata passed through from input | - |
reformated |
file | De-interleaved and standardized reads. For paired-end reads: _1_reformated and _2_reformated files. For single-end: *_reformated file. | *_reformated.{fastq,fq,fastq.gz,fq.gz,fasta,fa,fasta.gz,fa.gz} |
singleton |
file | Optional singleton reads from paired-end processing (reads where mate is missing). Only emitted for paired-end inputs. | *_singleton.{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 |
