bam_dedup_stats_samtools_umitools

UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats

umidedupindexbamsamcram

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/bam_dedup_stats_samtools_umitools

Description

UMI-tools dedup, index BAM file and run samtools stats, flagstat and idxstats

Input

name

description

pattern

`ch_bam_bai`

input BAM file
Structure: [ val(meta), path(bam), path(bai) ]

`val_get_dedup_stats`

Generate output stats when running “umi_tools dedup”

`val_primary_only`

Filter to primary alignments (SAM flag 0x900) before running UMI-tools dedup.
When true, secondary and supplementary alignments are removed so that dedup
statistics reflect only primary alignments.

Output

name

description

pattern

`bam`

Umi deduplicated BAM/SAM file
Structure: [ val(meta), path(bam) ]

`deduplog`

UMI-tools deduplication log
Structure: [ val(meta), path(log) ]

`tsv_edit_distance`

Reports the (binned) average edit distance between the UMIs at each position
Structure: [ val(meta), path(tsv) ]

`tsv_per_umi`

UMI-level summary statistics
Structure: [ val(meta), path(tsv) ]

`tsv_umi_per_position`

Tabulates the counts for unique combinations of UMI and position
Structure: [ val(meta), path(tsv) ]

`index`

Umi deduplicated BAM/SAM samtools index (BAI or CSI)
Structure: [ val(meta), path(bai/csi) ]

`stats`

File containing samtools stats output
Structure: [ val(meta), path(stats) ]

`flagstat`

File containing samtools flagstat output
Structure: [ val(meta), path(flagstat) ]

`idxstats`

File containing samtools idxstats output
Structure: [ val(meta), path(idxstats) ]