Read QC, UMI extraction and trimming
meta
Groovy Map containing sample information e.g. [ id:‘test’ ]
reads
List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively.
skip_fastqc
Skip fastqc process
with_umi
With or without umi detection
skip_umi_extract
With or without umi extrection
skip_trimming
Allows to skip trimgalore execution
umi_discard_read
Discard R1 / R2 if required
min_trimmed_reads
Inputs with fewer than this reads will be filtered out of the “reads” output channel
Extracted FASTQ files. | For single-end reads, pattern is ${prefix}.umi_extract.fastq.gz. |
For paired-end reads, pattern is ${prefix}.umi_extract_{1,2}.fastq.gz.
*.{fastq.gz}
fastqc_html
FastQC report
*_{fastqc.html}
fastqc_zip
FastQC report archive
*_{fastqc.zip}
log
Logfile for umi_tools
*.{log}
trim_unpaired
FastQ files containing unpaired reads from read 1 or read 2
*unpaired*.fq.gz
trim_html
FastQC report (optional)
trim_zip
FastQC report archive (optional)
trim_log
Trim Galore! trimming report
*_{report.txt}
trim_read_count
Number of reads remaining after trimming for all input samples
versions
File containing software versions
versions.yml
