bam_subsampledepth_samtools

Subsample a BAM/CRAM/SAM file using samtools to a given mean depth. “region”, “subsample_fraction”, “mean_depth” and “depth” keys will be added to the meta map to distinguish the different file generated and therefore shouldn’t be used. The depth key will be added to the meta map of the output channel.

subsamplebamsamcram

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

Description

Input

name

description

pattern

`ch_bam`

The input channel containing the BAM/CRAM/SAM files and their indexes.
Structure: [ val(meta), path(bam), path(bai) ]

*.{bam,cram,sam}

`ch_depth`

Target depth to downsample each input of ch_bam to.
Structure: [ val(meta), val(depth) ]
The meta map will be combined to the meta map of the ch_bam channel.

`ch_fasta`

The reference genome channel containing the fasta files and its index
Structure: [ val(meta), path(fasta), path(fai) ]

*.{fa(sta)?}

`ch_region`

An optional channel containing the different regions to consider
for the coverage calculation and downsampling.
Structure: [ val(meta), path(region) ]

*.bed

Output