Outputs Description

Files present after workflow is finished

Output File	Description
sample-name_fastp_out.html	Trimming metrics from fastp in html format
sample-name_fastp_out.json	Trimming metrics from fastp in json format
sample-name_fx.bam	Binary alignment map (BAM) file generated after FixMateInformation
sample-name_fx.bai	The binary alignment index (BAI) file associated with the FixMateInformation bam file
sample-name_duplication_metrics.txt	Metrics file for MarkDuplicated bam file.
sample-name_bqsr.bam	Final binary alignment map (BAM) file generated by the process
sample-name_bqsr.bai	The binary alignment index (BAI) file associated with the final bam.
sample-name_bqsr_alignment_summary_metrics.txt	Alignment Metrics on final uncollapsed BAM file
sample-name-collapsed_alignment_summary_metrics.txt	Collapsed alignment metrics
sample-name-duplex_alignment_summary_metrics.txt	Collapsed Duplex alignment metrics
sample-name-simplex_alignment_summary_metrics.txt	Collapsed Simplex alignment metrics
sample-name-duplex_family_sizes.txt	Duplex Family Size metrics
sample-name-duplex_umi_counts.txt	Duplex UMI count metrics
sample-name-duplex_yield_metrics.txt	Duplex yield metrics
sample-name-family_sizes.txt	UMI Family Size metrics
sample-name-umi_counts.txt	UMI Count metrics
sample-name-umi.hist.txt	UMI histogram file
sample-name-group.bam	Grouped BAM for duplex metrics calculation outside of the workflow
sample-name-collapsed.bam	Collapsed bam
sample-name-collapsed.bai	Collapsed bam index
sample-name-duplex.bam	Collapsed Duplex bam
sample-name-duplex.bai	Collapsed Duplex bam index
sample-name-simplex.bam	Collapsed Simplex bam
sample-name-simplex.bai	Collapsed Simplex bam index
collapsed_R1.fastq.gz	Collapsed Read 1 Fastq
collapsed_R2.fastq.gz	Collapsed Read 2 Fastq