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 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