Description

Read QC, UMI extraction and trimming

Input

name:type
description
pattern

meta :map

Groovy Map containing sample information
e.g. [ id:‘test’ ]

reads :file

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.

skip_fastqc :boolean

Skip fastqc process

with_umi :boolean

With or without umi detection

skip_umi_extract :boolean

With or without umi extrection

skip_trimming :boolean

Allows to skip trimgalore execution

umi_discard_read :integer

Discard R1 / R2 if required

min_trimmed_reads :integer

Inputs with fewer than this reads will be filtered out of the “reads” output channel

Output

name:type
description
pattern

reads :file

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 :file

FastQC report

*_{fastqc.html}

fastqc_zip :file

FastQC report archive

*_{fastqc.zip}

log :file

Logfile for umi_tools

*.{log}

trim_unpaired :file

FastQ files containing unpaired reads from read 1 or read 2

*unpaired*.fq.gz

trim_html :file

FastQC report (optional)

*_{fastqc.html}

trim_zip :file

FastQC report archive (optional)

*_{fastqc.zip}

trim_log :file

Trim Galore! trimming report

*_{report.txt}

trim_read_count :integer

Number of reads remaining after trimming for all input samples

versions :file

File containing software versions

versions.yml
included in
atacseq chipseq riboseq rnaseq rnasplice
included modules and subworkflows
fastqc umitools/extract trimgalore
maintainers
Github user drpatelh
Github user KamilMaliszArdigen
get in touch
Ask a question on Slack Open an issue on GitHub