Nextflow Registry | nf-core/sentieon/coveragemetrics@0.0.0-6c4ed3a

nf-core/sentieon/coveragemetrics @ 0.0.0-6c4ed3a

Accelerated implementation of the GATK DepthOfCoverage tool.

coverage sentieon genomics

Latest version: 0.0.0-6c4ed3a

Total downloads: 5

Source: nf-core/modules

Authors: @adamrtalbot

Maintainers: @adamrtalbot

Accelerated implementation of the GATK DepthOfCoverage tool.

Add the following snippet to your workflow script to include this module.

include { SENTIEON_COVERAGEMETRICS } from 'nf-core/sentieon/coveragemetrics'

MIT License

Process

`Name`	`SENTIEON_COVERAGEMETRICS`

Input 5 channels

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`bam` file	Sorted BAM/CRAM/SAM file `*.{bam,cram,sam}`
`bai` file	BAM/CRAM/SAM file index `*.{bai,crai}`

#2 tuple

`meta2` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`interval` file	BED file of genome regions to draw coverage from `*.bed`

#3 tuple

`meta3` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`fasta` file	Genome fasta file `*.{fa,fasta}`

#4 tuple

`meta4` map	Groovy Map containing sample information e.g. `[ id:'test', single_end:false ]`
`fai` file	Index of the genome fasta file `*.fai`

#5 tuple

`meta5` map	Groovy Map containing sample information e.g. [ id:'test', single_end:false ]
`gene_list` file	RefSeq file used to aggregate the results `*`

Output 7 channels

#1 per_locus tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}` file	The per locus coverage with no partition. `${sample_id}`

#2 statistics tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}.${partitions_output}_interval_statistics` file	The statistics for PARTITION_GROUP library, aggregated by interval. `${sample_id}_interval_statistics`

#3 sample_summary tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}.${partitions_output}_summary` file	The summary for PARTITION_GROUP sample, aggregated over all bases. `${sample_id}.sample_summary`

#4 coverage_counts tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}.${partitions_output}_cumulative_coverage_counts` file	Contains the histogram of loci with depth larger than x. `${sample_id}_cumulative_coverage_counts`

#5 interval_summary tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]`
`${prefix}.${partitions_output}_interval_summary` file	The summary for PARTITION_GROUP library, aggregated by interval. `${sample_id}_interval_summary`

#6 versions_sentieon tuple

`${task.process}` string	The process the versions were collected from
`sentieon` string	The tool name
`sentieon driver --version \| sed "s/.*-//g"` string	The command used to generate the version of the tool

#7 coverage_proportions tuple

`meta` map