Description

Preprocesses PacBio reads with optional LIMA demultiplexing, duplicate marking, and adapter trimming configured per input.

Input

Name
Description
Pattern

ch_reads (file)

PacBio reads with an optional per-input LIMA adapter file, a flag controlling duplicate marking, and an optional per-input HiFiTrimmer configuration YAML. Use an empty value for lima_adapter to skip LIMA. Use an empty value for adapter_yaml to skip adapter trimming for that input. Structure: [ val(meta), path(reads), path(lima_adapter), val(run_pbmarkdup), path(adapter_yaml) ]

*.(bam|fastq|fq|fasta|fa|fna)(.gz)?

val_hifi_adapter (file)

HiFi adapter BLAST database archive or FASTA used to build a database. An empty value disables adapter trimming.

*.(tar.gz|fasta|fa|fna)

Output

Name
Description
Pattern

untrimmed_fastx (file)

Channel containing preprocessed reads that are not filtered/trimmed with hifitrimmer in FASTA/FASTQ format. Structure: [ val(meta), path(fasta/fastq) ]

*.fasta|*.fa|*.fastq|*.fq

untrimmed_bam (file)

Channel containing preprocessed reads that are not filtered/trimmed with hifitrimmer in BAM format. Structure: [ val(meta), path(bam) ]

*.bam

trimmed_cram (file)

Channel containing preprocessed reads that have been filtered/trimmed with hifitrimmer in CRAM format. Structure: [ val(meta), path(cram) ]

*.cram

trimmed_bam (file)

Channel containing preprocessed reads that have been filtered/trimmed with hifitrimmer in BAM format. Structure: [ val(meta), path(bam) ]

*.bam

trimmed_sam (file)

Channel containing preprocessed reads that have been filtered/trimmed with hifitrimmer in SAM format. Structure: [ val(meta), path(sam) ]

*.sam

trimmed_fasta (file)

Channel containing preprocessed reads that have been filtered/trimmed with hifitrimmer in FASTA format. Structure: [ val(meta), path(fasta) ]

*.fasta|*.fa|*.fna

trimmed_fastq (file)

Channel containing preprocessed reads that have been filtered/trimmed with hifitrimmer in FASTQ format. Structure: [ val(meta), path(fastq) ]

*.fastq|*.fq

lima_report (file)

LIMA demultiplexing reports for reads supplied with a LIMA adapter. Structure: [ val(meta), path(report) ]

*.lima.report

lima_summary (file)

LIMA demultiplexing summaries for reads supplied with a LIMA adapter. Structure: [ val(meta), path(summary) ]

*.lima.summary

hifitrimmer_bed (file)

HiFiTrimmer adapter coordinates for reads with matching YAML configuration. Structure: [ val(meta), path(bed) ]

*.bed.gz

hifitrimmer_summary (file)

HiFiTrimmer summaries for reads with matching YAML configuration. Structure: [ val(meta), path(summary) ]

*.summary.json

pbmarkdup_stats (file)

pbmarkdup logs for reads with run_pbmarkdup set to true. Structure: [ val(meta), path(log) ]

*.pbmarkdup.log

Components

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