fastq_fastqc_umitools_fastp
Read QC, UMI extraction and trimming
Input
List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively, together with an optional fasta file of adapter sequences.
Structure: [ val(meta), [ path(reads) ], path(adapter_fasta) ]
*.{fastq.gz}Output
Trimmed FastQ files, UMI-extracted if requested, with samples below
min_trimmed_reads filtered out.
Structure: [ val(meta), [ path(reads) ] ]
*.{fastq.gz}FastQC report for the raw reads.
Structure: [ val(meta), [ path(html) ] ]
*_{fastqc.html}FastQC report archive for the raw reads.
Structure: [ val(meta), [ path(zip) ] ]
*_{fastqc.zip}UMI-extracted FastQ files, before trimming. | 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}Adapter sequence found in read1, parsed from the FastP JSON report.
Structure: [ val(meta), val(adapter_seq) ]
Trimmed fastq files failing QC.
Structure: [ val(meta), [ path(reads) ] ]
*.{fastq.gz}Trimmed and merged fastq files.
Structure: [ val(meta), [ path(reads) ] ]
*.{fastq.gz}FastQC report for the trimmed reads.
Structure: [ val(meta), [ path(html) ] ]
*_{fastqc.html}included modules and subworkflows
maintainer
