Nextflow Registry | nf-core/fgbio/collectduplexseqmetrics@0.0.0-6c4ed3a

nf-core/fgbio/collectduplexseqmetrics @ 0.0.0-6c4ed3a

Collects a suite of metrics to QC duplex sequencing data.

UMIs QC bam duplex

Latest version: 0.0.0-6c4ed3a

Total downloads: 6

Source: nf-core/modules

Authors: @georgiakes

Maintainers: @georgiakes

Collects a suite of metrics to QC duplex sequencing data.

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

include { FGBIO_COLLECTDUPLEXSEQMETRICS } from 'nf-core/fgbio/collectduplexseqmetrics'

MIT License

Process

`Name`	`FGBIO_COLLECTDUPLEXSEQMETRICS`

Input 1 channel

#1 tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`grouped_bam` file	It has to be either 1)The exact BAM output by the GroupReadsByUmi tool (in the sort-order it was produced in) 2)A BAM file that has MI tags present on all reads (usually set by GroupReadsByUmi and has been sorted with SortBam into TemplateCoordinate order. `*.bam`
`interval_list` file	Calculation of metrics may be restricted to a set of regions using the --intervals parameter. The file format is descripted here https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html `*.{tsv\|txt\|interval_list}`

Output 8 channels

#1 duplex_qc tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`**.duplex_qc.pdf` file	A series of plots generated from the preceding metrics files for visualization `*.pdf`

#2 umi_counts tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`**.umi_counts.txt` file	Metrics on the frequency of observations of UMIs within reads and tag families `*.txt`

#3 family_sizes tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`**.family_sizes.txt` file	Metrics on the frequency of different types of families of different sizes `*.txt`

#4 versions_fgbio tuple

`${task.process}` string	The process the versions were collected from
`fgbio` string	The tool name
`fgbio --version 2>&1 \| tr -d "[:cntrl:]" \| sed -e "s/^.Version: //;s/\[.$//"` eval	The command used to generate the version of the tool

#5 versions_ggplot2 tuple

`${task.process}` string	The process the versions were collected from
`ggplot2` string	The tool name
`Rscript -e "cat(as.character(packageVersion('ggplot2')))"` eval	The command used to generate the version of the tool

#6 duplex_umi_counts tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`**.duplex_umi_counts.txt` file	Metrics on the frequency of observations of duplex UMIs within reads and tag families. `*.txt`

#7 duplex_family_sizes tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`**.duplex_family_sizes.txt` file	Metrics on the frequency of duplex tag families by the number of observations from each strand `*.txt`

#8 duplex_yield_metrics tuple

`meta` map	Groovy Map containing sample information e.g. `[ id:'sample1' ]`
`**.duplex_yield_metrics.txt` file	Summary QC metrics produced using 5%, 10%, 15%...100% of the data `*.txt`

Tool	Description	Homepage
fgbio	A set of tools for working with genomic and high throughput sequencing data, including UMIs	http://fulcrumgenomics.github.io/fgbio/
r-ggplot2	ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.	https://ggplot2.tidyverse.org/

Version	0.0.0-6c4ed3a
Commit ID	6c4ed3a220310b905a1fc9d04f05be2e0837142b