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

umi_discard_read (integer)

Discard R1 / R2 if required

skip_trimming (boolean)

Allows to skip FastP execution

adapter_fasta (file)

Fasta file of adapter sequences

save_trimmed_fail (boolean)

Save trimmed fastqs of failed samples

save_merged (boolean)

Save merged fastqs

min_trimmed_reads (integer)

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

Output

Name (Type)
Description
Pattern

meta (map)

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

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_json (file)

FastP Trimming report

*.{fastp.json}

trim_html (file)

FastP Trimming report

*.{fastp.html}

log (file)

Logfile FastP

*.{fastp.log}

trim_reads_fail (file)

Trimmed fastq files failing QC

*.{fastq.gz}

trim_reads_merged (file)

Trimmed and merged fastq files

*.{fastq.gz}

trim_read_count (integer)

Number of reads after trimming

fastqc_trim_html (file)

FastQC report

*_{fastqc.html}

fastqc_trim_zip (file)

FastQC report archive

*_{fastqc.zip}

adapter_seq (string)

Adapter Sequence found in read1

versions (file)

File containing software versions

versions.yml
included in
riboseq rnaseq smrnaseq
included modules and subworkflows
fastqc umitools/extract fastp
maintainer
Github user robsyme
get in touch
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