fastq_fastqc_umitools_trimgalore
Read QC, UMI extraction and trimming
fastqfastqcqcUMItrimmingtrimgalore
Input
name
description
pattern
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
Structure: [ val(meta), [ path(reads) ] ]
*.{fastq.gz}Output
name
description
pattern
FastQ files after optional UMI extraction and adapter trimming, filtered on
the minimum trimmed read count.
Structure: [ val(meta), [ path(reads) ] ]
*.{fastq.gz}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. |
Structure: [ val(meta), [ path(reads) ] ]
*.{fastq.gz}FastQ files containing unpaired reads from read 1 or read 2.
Structure: [ val(meta), [ path(reads) ] ]
*unpaired*.fq.gzincluded modules and subworkflows
maintainers
