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
umi_discard_read
Discard R1 / R2 if required
skip_trimming
Allows to skip FastP execution
adapter_fasta
Fasta file of adapter sequences
save_trimmed_fail
Save trimmed fastqs of failed samples
save_merged
Save merged fastqs
min_trimmed_reads
Inputs with fewer than this reads will be filtered out of the “reads” output channel
Output
name
description
pattern
meta
Groovy Map containing sample information
e.g. [ id:‘test’ ]
reads
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.
