Perform adapter/quality trimming and QC on long sequencing reads (ONT, PacBio, etc.)
meta
:map
Groovy Map containing sample information. Use ‘single_end: true’ for single-end reads. e.g. [ id:‘test’, single_end:true ]
reads
:file
Input FASTQ file. Gzip-compressed files are supported.
*.{fastq.gz,fastq}
adapter_fasta
Optional FASTA file containing adapter sequences to trim.
*.{fasta,fa,fna}
discard_trimmed_pass
:boolean
If true, no reads that pass trimming thresholds will be written. Only reports will be generated.
save_trimmed_fail
If true, reads that fail filtering will be saved to a file ending in *.fail.fastq.gz.
*.fail.fastq.gz
Sample information map
*.fastplong.fastq.gz
Trimmed and filtered reads
*fastplong.fastq.gz
json
*.json
QC report in JSON format
html
*.html
QC report in HTML format
log
*.log
Log file generated during trimming
reads_fail
Reads that failed quality/trimming filters
*fail.fastq.gz
versions_fastplong
${task.process}
:string
The name of the process
fastplong
The name of the tool
fastplong --version 2>&1 | sed -e "s/fastplong //g"
:eval
The expression to obtain the version of the tool
versions
Ultra-fast preprocessing and quality control for long-read sequencing data.
